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This page provides a comprehensive list of all our academic and scientific peer-reviewed journal publications. We have added links to provide quick access to each paper.
582. Ashim Nandi, Aoxuan Zhang, Elad Arad, Raz Jelinek, and Arieh Warshel, Assessing the Catalytic Role of Native Glucagon Amyloid Fibrils, ACS Catalysis, 2024, 14, 4656-4664. doi: 10.1021/acscatal.4c00452
581. Rujuan Ti, Bin Pang, Yu Leiye, Bing Gan, Wenzhuo Ma, Arieh Warshel, Ruobing Ren, Lizhe Zhuand, Fine-tuning activation specificity of G-protein-coupled receptors via automated path searching, PNAS, 2024, 21(8):e2317893121. doi:10.1073/pnas.2317893121
580. Yue Zhang, Kang Wu, Yuqing Li, Song Wu, Arieh Warshel, and Chen Bai, Predicting Mutational Effects on Ca2+-Activated Chloride Conduction of TMEM16A Based on a Simulation Study, J. Am. Chem. Soc 2024. doi.org/10.1021/jacs.3c11940
579. An K, Yang X, Luo M, et al. Mechanistic study of the transmission pattern of the SARS-CoV-2 omicron variant. Proteins. 2024; 1-15. doi:10.1002/prot.26663
578. Jiao Zhou, Xiaohong Sang, Juan Wang, Yan Xu, Jing An, Zhen Tao Chu, Arjun Saha, Arieh Warshel, and Ziwei Huang, Elucidation of the α-Ketoamide Inhibition Mechanism: Revealing the Critical Role of the Electrostatic Reorganization Effect of Asp17 in the Active Site of the 20S Proteasome, ACS Catalysis 2023 13 (21), 14368-14376, doi: 10.1021/acscatal.3c03538.
577. A. Mojgan and A. Warshel, Analyzing the Reaction of Orotidine 5′-Phosphate Decarboxylase as a Way to Examine Some Key Catalytic Proposals, J. Am. Chem. Soc .145,1334-41 doi: 10.1021/jacs.2c11728(2023).
576. Giulio Vistoli, Candida Manelfi, Carmine Talarico, Anna Fava, Arieh Warshel, Igor V. Tetko, Rossen Apostolov, Yang Ye, Chiara Latini, Federico Ficarelli, Gianluca Palermo, Davide Gadioli, Emanuele Vitali, Gaetano Varriale, Vincenzo Pisapia, Marco Scaturro, Silvano Coletti, Daniele Gregori, Daniel Gruffat, Edgardo Leija, Sam Hessenauer, Alberto Delbianco, Marcello Allegretti and Andrea R. Beccari (2023) MEDIATE - Molecular DockIng at homE: Turning collaborative simulations into therapeutic solutions, Expert Opinion on Drug Discovery, 18:8, 821-833, doi: 10.1080/17460441.2023.2221025
575. Xie WJ, Liu D, Wang X, Zhang A, Wei Q, Nandi A, Dong S, Warshel A. Enhancing luciferase activity and stability through generative modeling of natural enzyme sequences. Proc Natl Acad Sci U S A. 2023 Nov 28;120(48):e2312848120. doi: 10.1073/pnas.2312848120. Epub 2023 Nov 20. PMID: 37983512; PMCID: PMC10691223.
574. Halder R, Warshel A. Energetic and structural insights behind calcium induced conformational transition in calmodulin. Proteins. 2023 Nov 1. doi: 10.1002/prot.26620. Epub ahead of print. PMID: 37915244.
573. D. Abbot et. al., In Defense of Merit in Science, Journal of Controversial Ideas, doi: 10.35995/jci03010001 (2023).
572. Wenjun Xie, Arieh Warshel, Harnessing natural evolution and computation towards systems enzymology, Biophysical Journal, Volume 122, Issue 3, Supplement 1, 2023, Page 462a, ISSN 0006-3495, doi: 10.1016/j.bpj.2022.11.2480
571. Asadi M, Xie WJ, Warshel A. Exploring the Role of Chemical Reactions in the Selectivity of Tyrosine Kinase Inhibitors. J Am Chem Soc. 2022 Sep 14;144(36):16638-16646. doi: 10.1021/jacs.2c07307. Epub 2022 Aug 31. PMID: 36044733; PMCID: PMC10387326.
570. Xie WJ, Warshel A. Natural Evolution Provides Strong Hints about Laboratory Evolution of Designer Enzymes. Proc Natl Acad Sci U S A. 2022 Aug 2;119(31):e2207904119. doi: 10.1073/pnas.2207904119. Epub 2022 Jul 28. PMID: 35901204; PMCID: PMC9351539.
569. Zhou J, Saha A, Huang Z, Warshel A. Fast and Effective Prediction of the Absolute Binding Free Energies of Covalent Inhibitors of SARS-CoV-2 Main Protease and 20S Proteasome. J Am Chem Soc. 2022 May 4;144(17):7568-7572. doi: 10.1021/jacs.2c00853. Epub 2022 Apr 18. PMID: 35436404; PMCID: PMC9359807.
568. Xie WJ, Xia S, Warshel A, Wu H. Electrostatic influence on IL-1 transport through the GSDMD pore. Proc Natl Acad Sci U S A. 2022 Feb 8;119(6):e2120287119. doi: 10.1073/pnas.2120287119. PMID: 35115408; PMCID: PMC8833203.
567. Xie WJ, Asadi M, Warshel A. Enhancing computational enzyme design by a maximum entropy strategy. Proc Natl Acad Sci U S A. 2022 Feb 15;119(7):e2122355119. doi: 10.1073/pnas.2122355119. PMID: 35135886; PMCID: PMC8851541.
566. Asadi M, Oanca G, Warshel A. Effect of Environmental Factors on the Catalytic Activity of Intramembrane Serine Protease. J Am Chem Soc. 2022 Jan 26;144(3):1251-1257.doi: 10.1021/jacs.1c10494. Epub 2022 Jan 13. PMID: 35023734.
565. A. Warshel, From Kibbutz Fishponds to the Nobel Prize; Taking Molecular Functions into Cyberspace, World Scientific (2021), doi:10.1142/12412 , November 2021.
564. Bai C, Wang J, Mondal D, Du Y, Ye RD, Warshel A. Exploring the Activation Process of the β2AR-Gs Complex. J Am Chem Soc. 2021 Jul 28;143(29):11044-11051. doi: 10.1021/jacs.1c03696. Epub 2021 Jul 13. PMID: 34255502..
563. C. Bai, J. Wang, G. K. Zhang, Ke An, P. Xu, Y. Du, R. D. Ye, A. Saha, A. Zhang, and A. Warshel, Predicting Mutational Effects on Receptor Binding of the SARS-CoV-2 Variants, Chen, J. Am. Chem. Soc.143,17646-17654 (2021). doi: 10.1073/pnas.1909032116. PCMID: PMC8525340.
562. A. Saha and A, Warshel, Simulating the Directional Translocation of a Substrate by the AAA+ Motor in the 26S Proteasome, 118 (23) e2104245118 doi:https://doi.org/10.1073/pnas.2104245118, Proc. Natl. Acad. Sci. USA, May 31, 2021
561. Wang J, Liang B, Chen Y, Fuk-Woo Chan J, Yuan S, Ye H, Nie L, Zhou J, Wu Y, Wu M, Huang LS, An J, Warshel A, Yuen KY, Ciechanover A, Huang Z, Xu Y. A new class of α-ketoamide derivatives with potent anticancer and anti-SARS-CoV-2 activities. Eur J Med Chem. 2021 Apr 5;215:113267, doi: 10.1016/j.ejmech.2021.113267, Epub 2021 Feb 10. PMID: 33639344; PMCID: PMC7873610.
560. Bai, C; Asadi, M; Warshel, A*; “The catalytic dwell in ATPases is not crucial for movement against applied torque”, Nature Chemistry, 2020, 12(12), 1187-1192, doi:10.1038/s41557-020-0549-6.
559. Oanca G, Asadi M, Saha A, Ramachandran B, Warshel A. Exploring the Catalytic Reaction of Cysteine Proteases. J Phys Chem B. 2020 Dec 17;124(50):11349-11356. doi: 10.1021/acs.jpcb.0c08192. Epub 2020 Dec 2. PMID: 33264018.
558. Mondal D, Warshel A. Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of α-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2. Biochemistry. 2020 Dec 8;59(48):4601-4608. doi: 10.1021/acs.biochem.0c00782. Epub 2020 Nov 18. PMID: 33205654; PMCID: PMC7688048.
557. Mondal D, Kolev V, Warshel A. Exploring the activation pathway and Gi-coupling specificity of the μ-opioid receptor. Proc Natl Acad Sci U S A. 2020 Oct 20;117(42):26218-26225. doi: 10.1073/pnas.2013364117. Epub 2020 Oct 5. PMID: 33020275; PMCID: PMC7585030.
556. C. Bai and A. Warshel, Critical Differences between the Binding Features of the Spike Proteins of Sars-Cov-2 and Sars-Cov, J. Phys. Chem. B, 124, 5907-5912 (2020).doi:10.1021/acs.jpcb.0c04317 PMCID: PMC7341686.
555. Saha A, Oanca G, Mondal D, Warshel A. Exploring the Proteolysis Mechanism of the Proteasomes. J Phys Chem B. 2020 Jul 9;124(27):5626-5635. doi: 10.1021/acs.jpcb.0c04435. Epub 2020 Jun 25. PMID: 32498514; PMCID: PMC7913600.
554. Mondal D, Kolev V, Warshel A. Combinatorial Approach for Exploring Conformational Space and Activation Barriers in Computer-Aided Enzyme Design. ACS Catal. 2020 Jun 5;10(11):6002-6012. doi: 10.1021/acscatal.0c01206. Epub 2020 Apr 27. PMID: 34178420; PMCID: PMC8225234.
553. Zhao LN, Mondal D, Warshel A. Exploring alternative catalytic mechanisms of the Cas9 HNH domain. Proteins. 2020 Feb;88(2):260-264. doi: 10.1002/prot.25796. Epub 2019 Sep 6. PMID: 31390092; PMCID: PMC6942198.
552. Alhadeff R, Warshel A. A free-energy landscape for the glucagon-like peptide 1 receptor GLP1R. Proteins. 2020 Jan;88(1):127-134. doi: 10.1002/prot.25777. Epub 2019 Aug 2. PubMed PMID: 31294890; PubMed Central PMCID: PMC6901726.
551. Mondal D, Florian J, Warshel A. Exploring the Effectiveness of Binding Free Energy Calculations. J Phys Chem B. 2019 Oct 24;123(42):8910-8915. doi: 10.1021/acs.jpcb.9b07593. Epub 2019 Oct 14. PubMed PMID: 31560539; PubMed Central PMCID: PMC7032235.
550. Bai C, Warshel A. Revisiting the protomotive vectorial motion of F0-ATPase. Proc Natl Acad Sci U S A. 2019 Sep 24;116(39):19484-19489. doi: 10.1073/pnas.1909032116. Epub 2019 Sep 11. PubMed PMID: 31511421; PubMed Central PMCID: PMC6765281.
549. Golan Y, Alhadeff R, Warshel A, Assaraf YG. ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion. PLoS Comput Biol. 2019 Mar;15(3):e1006882. doi: 10.1371/journal.pcbi.1006882. eCollection 2019 Mar. PubMed PMID: 30893306; PubMed Central PMCID: PMC6443192.
548. Alhadeff R, Warshel A. A free-energy landscape for the glucagon-like peptide 1 receptor GLP1R. Proteins. 2019 Jul 11;. doi: 10.1002/prot.25777. [Epub ahead of print] PubMed PMID: 31294890; PubMed Central PMCID: PMC6901726.
547. Jindal G, Slanska K, Kolev V, Damborsky J, Prokop Z, Warshel A. Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase. Proc Natl Acad Sci U S A. 2019 Jan 8;116(2):389-394. doi: 10.1073/pnas.1804979115. Epub 2018 Dec 26. PubMed PMID: 30587585; PubMed Central PMCID: PMC6329970.
546. Golan Y, Alhadeff R, Glaser F, Ganoth A, Warshel A, Assaraf YG. Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter. PLoS Comput Biol. 2018 Nov;14(11):e1006503. doi: 10.1371/journal.pcbi.1006503. eCollection 2018 Nov. PubMed PMID: 30388104; PubMed Central PMCID: PMC6241132.
545. Mondal D, Warshel A. (2018) EF-Tu and EF-G are activated by allosteric effects. Proc Natl Acad Sci U.S.A. 115(53):3386-3391, doi:10.1073/pnas.1800054115
544. Alhadeff R, Vorobyov I, Yoon HW, Warshel A. Exploring the free-energy landscape of GPCR activation. Proc Natl Acad Sci U S A. 2018 Oct 9;115(41):10327-10332. doi: 10.1073/pnas.1810316115. Epub 2018 Sep 26. PubMed PMID: 30257944; PubMed Central PMCID: PMC6187162.
543. Lee M, Kolev V, Warshel A. (2017) Validating a Coarse-Grained Voltage Activation Model by Comparing Its Performance to the Results of Monte Carlo Simulations. J Phys Chem B 121(50):11284-11291, doi:10.1021/acs.jpcb.7b09530
542. Jindal G, Ramachandran B, Bora RP, Warshel A. (2017) Exploring the Development of Ground-State Destabilization and Transition-State Stabilization in Two Directed Evolution Paths of Kemp Eliminases. ACS Catal 7(5):3301-3305, doi:10.1021/acscatal.7b00171
541. Yoon H, Kolev V, Warshel A. (2017) Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations. J Phys Chem B 121(40):9358-9365, doi:10.1021/acs.jpcb.7b07726
540. Jindal G, Warshel A. (2017) Misunderstanding the preorganization concept can lead to confusions about the origin of enzyme catalysis. Proteins 85(12):2157-2161, doi:10.1002/prot.25381
539. Alhadeff R, Warshel A. Reexamining the origin of the directionality of myosin V. Proc Natl Acad Sci U.S.A. 114(39):10426-10431, doi:10.1073/pnas.1711214114
538. Mukherjee S, Warshel A. (2017) The FOF1 ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function. Photosynth Res 134(1):1-15, doi:10.1007/s11120-017-0411-x
537. Jindal G, Mondal D, Warshel A. (2017) Exploring the Drug Resistance of HCV Protease. J Phys Chem B 121(28):6831-6840, doi:10.1021/acs.jpcb.7b04562
536. Roy S, Schopf P, Warshel A. (2017) Origin of the Non-Arrhenius Behavior of the Rates of Enzymatic Reactions. J Phys Chem B 121(27):6520-6526, doi:10.1021/acs.jpcb.7b03698
535. Yoon H, Warshel A. (2017) Simulating the fidelity and the three Mg mechanism of pol η and clarifying the validity of transition state theory in enzyme catalysis. Proteins 85(8):1446-1453, doi:10.1002/prot.25305
534. Mukherjee S, Alhadeff R, Warshel A. (2017) Simulating the dynamics of the mechanochemical cycle of myosin-V. Proc Natl Acad Sci U.S.A. 114(9):2259-2264, doi:10.1073/pnas.1700318114
533. Matute RA, Yoon H, Warshel A. (2016) Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β. Proteins 84(11):1644-1657, doi:10.1002/prot.25106
532. Yoon H, Warshel A. (2016) The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase. Proteins 84(11):1616-1624, doi:10.1002/prot.25104
531. Alhadeff R, Warshel A. (2016) Simulating the Function of the MjNhaP1 Transporter. J Phys Chem B 120(42),10951–10958, doi:10.1021/acs.jpcb.6b08126
530. Jindal G, Warshel A. (2016) Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region. J Phys Chem B 120(37):9913-21, doi:10.1021/acs.jpcb.6b07203
529. Kim I, Warshel A. (2016) Analyzing the electrogenicity of cytochrome c oxidase. Proc Natl Acad Sci U.S.A. 113(28):7810-5, doi:10.1073/pnas.1608118113
528. Warshel A, Bora RP. (2016) Perspective: Defining and quantifying the role of dynamics in enzyme catalysis. J Chem Phys 144(18):180901, doi:10.1063/1.4947037
527. stumian RD, Mukherjee S, Warshel A. (2016) The Physics and Physical Chemistry of Molecular Machines. Chemphyschem 17(12):1719-41, doi:10.1002/cphc.201600184
526. Lameira J, Kupchencko I & Warshel A (2016) Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions. J Phys Chem B 120(9):2155-64, doi:10.1021/acs.jpcb.5b11966
525. Kim I & Warshel A (2016) A Microscopic Capacitor Model of Voltage Coupling in Membrane Proteins: Gating Charge Fluctuations in Ci-VSD. J Phys Chem B 120(3):418-32, doi:10.1021/acs.jpcb.5b10956
524. Mukherjee S, Bora RP & Warshel A (2015) Torque, chemistry and efficiency in molecular motors: a study of the rotary-chemical coupling in F1-ATPase. Q Rev Biophys 48(4):395-403, doi:10.1017/S0033583515000050
523. Vorobyov I, Kim I, Chu ZT & Warshel A (2015) Refining the treatment of membrane proteins by coarse-grained models. Proteins 84(1):92-117, doi:10.1002/prot.24958
522. Mukherjee S & Warshel A (2015) Brønsted slopes based on single-molecule imaging data help to unveil the chemically coupled rotation in F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America 112:14121-2, doi:10.1073/pnas.1519066112
521. Alhadeff R & Warshel A (2015) Simulating the function of sodium/proton antiporters. Proceedings of the National Academy of Sciences of the United States of America 112(40):12378-83, doi:10.1073/pnas.1516881112
520. Kim I & Warshel A (2015) Equilibrium fluctuation relations for voltage coupling in membrane proteins. Biochim Biophys Acta 1848:2985-97, doi:10.1016/j.bbamem.2015.08.008
519. Schopf P, Mills MJ & Warshel A (2015) The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm. Proceedings of the National Academy of Sciences of the United States of America 112(14):4328-33, doi:10.1073/pnas.1503828112
518. S. Mukherjee & A. Warshel (2015) Dissecting the role of the γ-subunit in the rotary-chemical coupling and torque generation of F1-ATPase. Proceedings of the National Academy of Sciences of the United States of America 112:2746-2751, doi:10.1073/pnas.1500979112
517. Bora RP, Mills MJ, Frushicheva MP & Warshel A. (2015) On the challenge of exploring the evolutionary trajectory from phosphotriesterase to arylesterase using computer simulations. J Phys Chem B 119(8):3434-45, doi:10.1021/jp5124025
516. J. Lameira, R.B. Prasad, Z.T. Chu & A. Warshel (2014) Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization. Proteins 83:318-330, doi:10.1002/prot.24717
515. M.K. Singh, Z.T. Chu & A. Warshel (2014) Simulating the Catalytic Effect of a Designed Mononuclear Zinc Metalloenzyme that Catalyzes the Hydrolysis of Phosphate Triesters. Phys Chem. B 118:12146-12152, doi:10.1021/jp507592g
514. A. Warshel (2014) Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture). Angew. Chem. 53:10020-10031, doi:10.1002/anie.201403689
513. M.P. Frushicheva, M.J.L. Mills, P. Schopf, M.K. Singh, R.B. Prasad & A. Warshel (2014) Computer Aided Enzyme Design and Catalytic Concepts. Curr. Opin. Chem. Biol. 21:56-62, doi:10.1016/j.cbpa.2014.03.022
512. I. Kim, S. Chakrabarty, P. Brzezinski & A. Warshel (2014) Modeling Gating Charge and Voltage Changes in Response to Charge Separation in Membrane Proteins. Proceedings of the National Academy of Sciences of the United States of America 111:11353-11358, doi:10.1073/pnas.1411573111
511. P. Schopf & A. Warshel (2014) Validating Computer Simulations of Enantioselective Catalysis; Reproducing the Large Steric and Entropic Contributions in Candida Antarctica Lipase B. Proteins 82:1387-1399, doi:10.1002/prot.24506
510. S. Vicatos, A. Rychkova, S. Mukherjee & A. Warshel (2014) An Effective Coarse-Grained Model for Biological Simulations: Recent Refinements and Validations. Proteins 82:1168-1185, doi:10.1002/prot.24482
509. S. Mukherjee & A. Warshel (2014) Response to Vilfan: Constructing Structure-Based Free Energy Surfaces is the Key to Understand Myosin V Unidirectionality. Proceedings of the National Academy of Sciences of the United States of America 111:2077, doi:10.1073/pnas.1404542111
508. A. Warshel (2013) How do Enzymes Really Work? The The Dawn of Simulating Biological Functions (1974–5) Memories and Consequences: Visiting Scientists at the MRC Laboratory of Molecular Biology, Cambridge. Published by MRC, ed. H. Huxley, 33:271-281.
507. I. Kim & A. Warshel (2013) Coarse-Grained Simulation of the Gating Current in the Voltage-Activation Kv1.2 Channel. Proceedings of the National Academy of Sciences of the United States of America 111:2128-2133, doi:10.1073/pnas.1324014111
506. R.B. Prasad, N.V. Plotnikov, J. Lameira & A. Warshel (2013) Quantitative exploration of the molecular origin of the activation of GTPase. Proceedings of the National Academy of Sciences of the United States of America 110(51):20509, doi:10.1037/pnas.1319854110
504. A. Warshel & M. Karplus (2013) Semiclassical Trajectory Approach to Photoisomerization (Reprinted from Chemical Physics Letters, Vol 32, Pg 11-17, 1975). Chemical Physics Letters 589:68, doi:10.1016/j.cplett.2013.10.028.
503. A. Warshel (2013) Using Cg Modeling in Exploring the Role of Dynamical Effects in Catalysis and in Simulating Biological Molecular Machines. Journal of Biomolecular Structure & Dynamics 31:121, doi:10.1080/07391102.2013.786430.
502. A. Rychkova & A. Warshel (2013) Exploring the Nature of the Translocon-Assisted Protein Insertion. Proceedings of the National Academy of Sciences of the United States of America 110(2):495, doi:10.1073/pnas.1220361110.
501. A. Rychkova & A. Warshel (2013) On the Nature of the Apparent Free Energy of Inserting Amino Acids into Membrane through the Translocon. Journal of Physical Chemistry B 117(44):13748, doi:10.1021/jp406925y.
500. A. Rychkova, S. Mukherjee, R. P. Bora, & A. Warshel (2013) Simulating the Pulling of Stalled Elongated Peptide from the Ribosome by the Translocon. Proceedings of the National Academy of Sciences of the United States of America 110(25):10195, doi:10.1073/pnas.1307869110.
499. R. B. Prasad, N. V. Plotnikov, J. Lameira, & A. Warshel (2013) Quantitative Exploration of the Molecular Origin of the Activation of Gtpase. Proceedings of the National Academy of Sciences of the United States of America 110(51):20509, doi:10.1073/pnas.1319854110.
498. B. R. Prasad, N. V. Plotnikov, & A. Warshel (2013) Addressing Open Questions About Phosphate Hydrolysis Pathways by Careful Free Energy Mapping. Journal of Physical Chemistry B 117(1):153, doi:10.1021/jp309778n.
497. N. V. Plotnikoy, B. R. Prasad, S. Chakrabarty, Z. T. Chu, & A. Warshel (2013) Quantifying the Mechanism of Phosphate Monoester Hydrolysis in Aqueous Solution by Evaluating the Relevant Ab Initio Qm/Mm Free-Energy Surfaces. Journal of Physical Chemistry B 117(42):12807, doi:10.1021/jp4020146.
496. S. Mukherjee & A. Warshel (2013) Electrostatic Origin of the Unidirectionality of Walking Myosin V Motors. Proceedings of the National Academy of Sciences of the United States of America 110(43):17326, doi:10.1073/pnas.1317641110.
495. S. C. L. Kamerlin, P. K. Sharma, R. B. Prasad, & A. Warshel (2013) Why Nature Really Chose Phosphate. Quarterly Reviews of Biophysics 46(1):1, doi:10.1017/s0033583512000157.
494. S. Chakrabarty & A. Warshel (2013) Capturing the Energetics of Water Insertion in Biological Systems: The Water Flooding Approach. Proteins-Structure Function and Bioinformatics 81(1):93, doi:10.1002/prot.24165.
489. N. Singh, M. P. Frushicheva, & A. Warshel (2012) Validating the Vitality Strategy for Fighting Drug Resistance. Proteins-Structure Function and Bioinformatics 80(4):1110, doi:10.1002/prot.24012.
487. E. Rosta & A. Warshel (2012) Origin of Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in S(N)2 Reactions. Journal of Chemical Theory and Computation 8(10):3574, doi:10.1021/ct2009329.
486. B. R. Prasad, S. C. L. Kamerlin, J. Florian, & A. Warshel (2012) Prechemistry Barriers and Checkpoints Do Not Contribute to Fidelity and Catalysis as Long as They Are Not Rate Limiting. Theoretical Chemistry Accounts 131(12), doi:10.1007/s00214-012-1288-6.
484. N. V. Plotnikov & A. Warshel (2012) Exploring, Refining, and Validating the Paradynamics Qm/Mm Sampling. Journal of Physical Chemistry B 116(34):10342, doi:10.1021/jp304678d.
481. S. Mukherjee & A. Warshel (2012) Realistic Simulations of the Coupling between the Protomotive Force and the Mechanical Rotation of the F-0-Atpase. Proceedings of the National Academy of Sciences of the United States of America 109(37):14876, doi:10.1073/pnas.1212841109.
480. M. Klvana, D. L. Murphy, P. Jerabek, M. F. Goodman, A. Warshel, J. B. Sweasy, & J. Florian (2012) Catalytic Effects of Mutations of Distant Protein Residues in Human DNA Polymerase Beta: Theory and Experiment. Biochemistry 51(44):8829, doi:10.1021/bi300783t.
479. M. P. Frushicheva & A. Warshel (2012) Towards Quantitative Computer-Aided Studies of Enzymatic Enantioselectivity: The Case of Candida Antarctica Lipase A. Chembiochem 13(2):215, doi:10.1002/cbic.201100600.
477. M. P. Frushicheva, S. Mukherjee, & A. Warshel (2012) Electrostatic Origin of the Catalytic Effect of a Supramolecular Host Catalyst. Journal of Physical Chemistry B 116(45):13353, doi:10.1021/jp3084327.
474. A. Dryga, S. Chakrabarty, S. Vicatos, & A. Warshel (2012) Coarse Grained Model for Exploring Voltage Dependent Ion Channels. Biochimica Et Biophysica Acta-Biomembranes 1818(2):303, doi:10.1016/j.bbamem.2011.07.043.
473. A. Dryga, S. Chakrabarty, S. Vicatos, & A. Warshel (2012) Realistic Simulation of the Activation of Voltage-Gated Ion Channels. Proceedings of the National Academy of Sciences of the United States of America 109(9):3335, doi:10.1073/pnas.1121094109.
471. A. Warshel & A. Dryga (2011) Simulating Electrostatic Energies in Proteins: Perspectives and Some Recent Studies of Pk(a)S, Redox, and Other Crucial Functional Properties. Proteins-Structure Function and Bioinformatics 79(12):3469, doi:10.1002/prot.23125.
467. B. R. Prasad & A. Warshel (2011) Prechemistry Versus Preorganization in DNA Replication Fidelity. Proteins-Structure Function and Bioinformatics 79(10):2900, doi:10.1002/prot.23128.
466. N. V. Plotnikov, S. C. L. Kamerlin, & A. Warshel (2011) Paradynamics: An Effective and Reliable Model for Ab Lnitio Qm/Mm Free-Energy Calculations and Related Tasks. Journal of Physical Chemistry B 115(24):7950, doi:10.1021/jp201217b.
463. S. Mukherjee & A. Warshel (2011) Electrostatic Origin of the Mechanochemical Rotary Mechanism and the Catalytic Dwell of F1-Atpase. Proceedings of the National Academy of Sciences of the United States of America 108(51):20550, doi:10.1073/pnas.1117024108.
462. S. C. L. Kamerlin & A. Warshel (2011) The Empirical Valence Bond Model: Theory and Applications. Wiley Interdisciplinary Reviews-Computational Molecular Science 1(1):30, doi:10.1002/wcms.10.
461. S. C. L. Kamerlin & A. Warshel (2011) Multiscale Modeling of Biological Functions. Physical Chemistry Chemical Physics 13(22):10401, doi:10.1039/c0cp02823a.
460. S. C. L. Kamerlin, S. Vicatos, A. Dryga, & A. Warshel (2011) Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems. Annual Review of Physical Chemistry, Vol 62, Annual Review of Physical Chemistry, eds Leone SR, Cremer PS, Groves JT, & Johnson MA), Vol 62, pp 41.doi: 10.1146/annurev-physchem-032210-103335
459. A.-L. Johansson, S. Chakrabarty, C. L. Berthold, M. Hogbom, A. Warshel, & P. Brzezinski (2011) Proton-Transport Mechanisms in Cytochrome C Oxidase Revealed by Studies of Kinetic Isotope Effects. Biochimica Et Biophysica Acta-Bioenergetics 1807(9):1083, doi:10.1016/j.bbabio.2011.03.012.
455. M. P. Frushicheva, J. Cao, & A. Warshel (2011) Challenges and Advances in Validating Enzyme Design Proposals: The Case of Kemp Eliminase Catalysis. Biochemistry 50(18):3849, doi:10.1021/bi200063a.
452. S. Chakrabarty, I. Namslauer, P. Brzezinski, & A. Warshel (2011) Exploration of the Cytochrome C Oxidase Pathway Puzzle and Examination of the Origin of Elusive Mutational Effects. Biochimica Et Biophysica Acta-Bioenergetics 1807(4):413, doi:10.1016/j.bbabio.2011.01.004.
449. A. J. Adamczyk & A. Warshel (2011) Converting Structural Information into an Allosteric-Energy-Based Picture for Elongation Factor Tu Activation by the Ribosome. Proceedings of the National Academy of Sciences of the United States of America 108(24):9827, doi:10.1073/pnas.1105714108.
448. A. J. Adamczyk, J. Cao, S. C. L. Kamerlin, & A. Warshel (2011) Catalysis by Dihydrofolate Reductase and Other Enzymes Arises from Electrostatic Preorganization, Not Conformational Motions. Proceedings of the National Academy of Sciences of the United States of America 108(34):14115, doi:10.1073/pnas.1111252108.
447. N. Singh & A. Warshel (2010) A Comprehensive Examination of the Contributions to the Binding Entropy of Protein-Ligand Complexes. Proteins-Structure Function and Bioinformatics 78(7):1724, doi:10.1002/prot.22689.
446. N. Singh & A. Warshel (2010) Absolute Binding Free Energy Calculations: On the Accuracy of Computational Scoring of Protein-Ligand Interactions. Proteins-Structure Function and Bioinformatics 78(7):1705, doi:10.1002/prot.22687.
445. A. Rychkova, S. Vicatos, & A. Warshel (2010) On the Energetics of Translocon-Assisted Insertion of Charged Transmembrane Helices into Membranes. Proceedings of the National Academy of Sciences of the United States of America 107(41):17598, doi:10.1073/pnas.1012207107.
444. R. Rucker, P. Oelschlaeger, & A. Warshel (2010) A Binding Free Energy Decomposition Approach for Accurate Calculations of the Fidelity of DNA Polymerases. Proteins-Structure Function and Bioinformatics 78(3):671, doi:10.1002/prot.22596.
442. A. Pisliakov, Y. Sugita, & A. Warshel (2010) Computer Simulations of Proton Transfer in Cytochrome C Oxidase and Nitric Oxide Reductase. Biochimica Et Biophysica Acta-Bioenergetics 1797:99, doi:10.1016/j.bbabio.2010.04.300.
441. B. M. Messer, M. Roca, Z. T. Chu, S. Vicatos, A. V. Kilshtain, & A. Warshel (2010) Multiscale Simulations of Protein Landscapes: Using Coarse-Grained Models as Reference Potentials to Full Explicit Models. Proteins-Structure Function and Bioinformatics 78(5):1212, doi:10.1002/prot.22640.
440. S. C. L. Kamerlin & A. Warshel (2010) The Evb as a Quantitative Tool for Formulating Simulations and Analyzing Biological and Chemical Reactions. Faraday Discussions 145:71, doi:10.1039/b907354j.
439. S. C. L. Kamerlin & A. Warshel (2010) Reply to Karplus: Conformational Dynamics Have No Role in the Chemical Step. Proceedings of the National Academy of Sciences of the United States of America 107(17):E72, doi:10.1073/pnas.1002658107.
438. S. C. L. Kamerlin & A. Warshel (2010) At the Dawn of the 21st Century: Is Dynamics the Missing Link for Understanding Enzyme Catalysis? Proteins-Structure Function and Bioinformatics 78(6):1339, doi:10.1002/prot.22654.
437. S. C. L. Kamerlin & A. Warshel (2010) An Analysis of All the Relevant Facts and Arguments Indicates That Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling. Journal of Physical Organic Chemistry 23(7):677, doi:10.1002/poc.1620.
436. S. C. L. Kamerlin, P. K. Sharma, Z. T. Chu, & A. Warshel (2010) Ketosteroid Isomerase Provides Further Support for the Idea That Enzymes Work by Electrostatic Preorganization. Proceedings of the National Academy of Sciences of the United States of America 107(9):4075, doi:10.1073/pnas.0914579107.
435. S. C. L. Kamerlin, J. Mavri, & A. Warshel (2010) Examining the Case for the Effect of Barrier Compression on Tunneling, Vibrationally Enhanced Catalysis, Catalytic Entropy and Related Issues. Febs Letters 584(13):2759, doi:10.1016/j.febslet.2010.04.062.
434. S. C. L. Kamerlin, Z. T. Chu, & A. Warshel (2010) On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems with the Gas-Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models. Journal of Organic Chemistry 75(19):6391, doi:10.1021/jo100651s.
432. M. P. Frushicheva, J. Cao, Z. T. Chu, & A. Warshel (2010) Exploring Challenges in Rational Enzyme Design by Simulating the Catalysis in Artificial Kemp Eliminase. Proceedings of the National Academy of Sciences of the United States of America 107(39):16869, doi:10.1073/pnas.1010381107.
431. A. Dryga & A. Warshel (2010) Renormalizing Smd: The Renormalization Approach and Its Use in Long Time Simulations and Accelerated Pau Calculations of Macromolecules. Journal of Physical Chemistry B 114(39):12720, doi:10.1021/jp1056122.
430. A. Alkherraz, S. C. L. Kamerlin, G. Feng, Q. I. Sheikh, A. Warshel, & N. H. Williams (2010) Phosphate Ester Analogues as Probes for Understanding Enzyme Catalysed Phosphoryl Transfer. Faraday Discussions 145:281, doi:10.1039/b908398g.
427. S. Vicatos, M. Roca, & A. Warshel (2009) Effective Approach for Calculations of Absolute Stability of Proteins Using Focused Dielectric Constants. Proteins-Structure Function and Bioinformatics 77(3):670, doi:10.1002/prot.22481.
426. A. Vardi-Kilshtain, M. Roca, & A. Warshel (2009) The Empirical Valence Bond as an Effective Strategy for Computer-Aided Enzyme Design. Biotechnology Journal 4(4):495, doi:10.1002/biot.200800299.
425. N. Singh & A. Warshel (2009) Toward Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects. Journal of Physical Chemistry B 113(20):7372, doi:10.1021/jp811063v.
424. M. Roca, A. Vardi-Kilshtain, & A. Warshel (2009) Toward Accurate Screening in Computer-Aided Enzyme Design. Biochemistry 48(14):3046, doi:10.1021/bi802191b.
422. A. V. Pisliakov, J. Cao, S. C. L. Kamerlin, & A. Warshel (2009) Enzyme Millisecond Conformational Dynamics Do Not Catalyze the Chemical Step. Proceedings of the National Academy of Sciences of the United States of America 106(41):17359, doi:10.1073/pnas.0909150106.
421. W. W. Parson & A. Warshel (2009) Mechanism of Charge Separation in Purple Bacterial Reaction Centers pp 355.
420. H. Liu & A. Warshel (2009) Tunnelling Does Not Contribute Significantly to Enzyme Catalysis, but Studying Temperature Dependence of Isotope Effects Is Useful pp 242, doi:10.1039/9781847559975-00242.
419. H. Liu, Y. Shi, X. S. Chen, & A. Warshel (2009) Simulating the Electrostatic Guidance of the Vectorial Translocations in Hexameric Helicases and Translocases. Proceedings of the National Academy of Sciences of the United States of America 106(18):7449, doi:10.1073/pnas.0900532106.
418. A. V. Kilshtain & A. Warshel (2009) On the Origin of the Catalytic Power of Carboxypeptidase a and Other Metalloenzymes. Proteins-Structure Function and Bioinformatics 77(3):536, doi:10.1002/prot.22466.
417. S. C. L. Kamerlin & A. Warshel (2009) On the Energetics of Atp Hydrolysis in Solution. Journal of Physical Chemistry B 113(47):15692, doi:10.1021/jp907223t.
416. S. C. L. Kamerlin, C. E. Mckenna, M. F. Goondman, & A. Warshel (2009) A Computational Study of the Hydrolysis of Dgtp Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases. Biochemistry 48(25):5963, doi:10.1021/bi900140c.
415. S. C. L. Kamerlin, C. E. Mckenna, M. F. Goodman, & A. Warshel (2009) A Computational Study of the Hydrolysis of Dgtp Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases (Vol 48, Pg 5963, 2009). Biochemistry 48(32):7776, doi:10.1021/bi901141c.
414. S. C. L. Kamerlin, M. Haranczyk, & A. Warshel (2009) Progress in Ab Initio Qm/Mm Free-Energy Simulations of Electrostatic Energies in Proteins: Accelerated Qm/Mm Studies of Pk(a), Redox Reactions and Solvation Free Energies. Journal of Physical Chemistry B 113(5):1253, doi:10.1021/jp8071712.
413. S. C. L. Kamerlin, M. Haranczyk, & A. Warshel (2009) Are Mixed Explicit/Implicit Solvation Models Reliable for Studying Phosphate Hydrolysis? A Comparative Study of Continuum, Explicit and Mixed Solvation Models. Chemphyschem 10(7):1125, doi:10.1002/cphc.200800753.
412. S. C. L. Kamerlin, J. Cao, E. Rosta, & A. Warshel (2009) On Unjustifiably Misrepresenting the Evb Approach While Simultaneously Adopting It. Journal of Physical Chemistry B 113(31):10905, doi:10.1021/jp901709f.
411. Y. Xiang & A. Warshel (2008) Quantifying Free Energy Profiles of Proton Transfer Reactions in Solution and Proteins by Using a Diabatic Fdft Mapping. Journal of Physical Chemistry B 112(3):1007, doi:10.1021/jp076931f.
410. Y. Xiang, M. F. Goodman, W. A. Beard, S. H. Wilson, & A. Warshel (2008) Exploring the Role of Large Conformational Changes in the Fidelity of DNA Polymerase Beta. Proteins-Structure Function and Bioinformatics 70(1):231, doi:10.1002/prot.21668.
409. C. A. Sucato, T. G. Upton, B. A. Kashemirov, J. Osuna, K. Oertell, W. A. Beard, S. H. Wilson, J. Florian, A. Warshel, C. E. Mckenna, & M. F. Goodman (2008) DNA Polymerase Beta Fidelity: Halomethylene-Modified Leaving Groups in Pre-Steady-State Kinetic Analysis Reveal Differences at the Chemical Transition State. Biochemistry 47(3):870, doi:10.1021/bi7014162.
408. E. Rosta, S. C. L. Kamerlin, & A. Warshel (2008) On the Interpretation of the Observed Linear Free Energy Relationship in Phosphate Hydrolysis: A Thorough Computational Study of Phosphate Diester Hydrolysis in Solution. Biochemistry 47(12):3725, doi:10.1021/bi702106m.
407. E. Rosta, M. Haranczyk, Z. T. Chu, & A. Warshel (2008) Accelerating Qm/Mm Free Energy Calculations: Representing the Surroundings by an Updated Mean Charge Distribution. Journal of Physical Chemistry B 112(18):5680, doi:10.1021/jp711496y.
406. M. Roca, B. Messer, D. Hilvert, & A. Warshel (2008) On the Relationship between Folding and Chemical Landscapes in Enzyme Catalysis. Proceedings of the National Academy of Sciences of the United States of America 105(37):13877, doi:10.1073/pnas.0803405105.
405. A. V. Pisliakov, P. K. Sharma, Z. T. Chu, M. Haranczyk, & A. Warshel (2008) Electrostatic Basis for the Unidirectionality of the Primary Proton Transfer in Cytochrome C Oxidase. Proceedings of the National Academy of Sciences of the United States of America 105(22):7726, doi:10.1073/pnas.0800580105.
404. W. W. Parson & A. Warshel (2008) Calculations of Electrostatic Energies in Proteins Using Microscopic, Semimicroscopic and Macroscopic Models and Free-Energy Perturbation Approaches pp 401.doi.org/10.1021/ja00154a031
403. J. Mavri, H. Liu, M. H. M. Olsson, & A. Warshel (2008) Simulation of Tunneling in Enzyme Catalysis by Combining a Biased Propagation Approach and the Quantum Classical Path Method: Application to Lipoxygenase. Journal of Physical Chemistry B 112(19):5950, doi:10.1021/jp0758420.
402. M. Kato, S. Braun-Sand, & A. Warshel (2008) Challenges and Progresses in Calculations of Binding Free Energies - What Does It Take to Quantify Electrostatic Contributions to Protein-Ligand Interactions? pp 268.
401. S. C. L. Kamerlin, N. H. Williams, & A. Warshel (2008) Dineopentyl Phosphate Hydrolysis: Evidence for Stepwise Water Attack. Journal of Organic Chemistry 73(18):6960, doi:10.1021/jo801207q.
400. S. C. L. Kamerlin, J. Florian, & A. Warshel (2008) Associative Versus Dissociative Mechanisms of Phosphate Monoester Hydrolysis: On the Interpretation of Activation Entropies. Chemphyschem 9(12):1767, doi:10.1002/cphc.200800356.
399. H. Ishikita & A. Warshel (2008) Predicting Drug-Resistant Mutations of Hiv Protease. Angewandte Chemie-International Edition 47(4):697, doi:10.1002/anie.200704178.
398. M. Haranczyk, M. Gutowski, & A. Warshel (2008) Solvation Free Energies of Molecules. The Most Stable Anionic Tautomers of Uracil. Physical Chemistry Chemical Physics 10(30):4442, doi:10.1039/b802300j.
397. S. Braun-Sand, P. K. Sharma, Z. T. Chu, A. V. Pisliakov, & A. Warshel (2008) The Energetics of the Primary Proton Transfer in Bacteriorhodopsin Revisited: It Is a Sequential Light-Induced Charge Separation after All. Biochimica Et Biophysica Acta-Bioenergetics 1777(5):441, doi:10.1016/j.bbabio.2008.03.001.
396. A. Warshel, P. K. Sharma, Z. T. Chu, & J. Aqvist (2007) Electrostatic Contributions to Binding of Transition State Analogues Can Be Very Different from the Corresponding Contributions to Catalysis: Phenolates Binding to the Oxyanion Hole of Ketosteroid Isomerase. Biochemistry 46(6):1466, doi:10.1021/bi061752u.
395. A. Warshel, M. Kato, & A. V. Pisliakov (2007) Polarizable Force Fields: History, Test Cases, and Prospects. Journal of Chemical Theory and Computation 3(6):2034, doi:10.1021/ct700127w.
390. C. A. Sucato, T. G. Upton, B. A. Kashemirov, V. K. Batra, V. Martinek, Y. Xiang, W. A. Beard, L. C. Pedersen, S. H. Wilson, C. E. Mckenna, J. Florian, A. Warshel, & M. F. Goodman (2007) Modifying the Beta,Gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase Beta. Biochemistry 46(2):461, doi:10.1021/bi061517b.
389. P. K. Sharma, Z. T. Chu, M. H. M. Olsson, & A. Warshel (2007) A New Paradigm for Electrostatic Catalysis of Radical Reactions in Vitamin B-12 Enzymes. Proceedings of the National Academy of Sciences of the United States of America 104(23):9661, doi:10.1073/pnas.0702238104.
388. M. Roca, B. Messer, & A. Warshel (2007) Electrostatic Contributions to Protein Stability and Folding Energy. Febs Letters 581(10):2065, doi:10.1016/j.febslet.2007.04.025.
387. M. Roca, H. Liu, B. Messer, & A. Warshel (2007) On the Relationship between Thermal Stability and Catalytic Power of Enzymes. Biochemistry 46(51):15076, doi:10.1021/bi701732a.
386. M. H. M. Olsson, P. E. M. Slegbahn, M. R. A. Blomberg, & A. Warshel (2007) Exploring Pathways and Barriers for Coupled Et/Pt in Cytochrome C Oxidase: A General Framework for Examining Energetics and Mechanistic Alternatives. Biochimica Et Biophysica Acta-Bioenergetics 1767(3):244, doi:10.1016/j.bbabio.2007.01.015.
385. P. Oelschlaeger, M. Klahn, W. A. Beard, S. H. Wilson, & A. Warshel (2007) Magnesium-Cationic Dummy Atom Molecules Enhance Representation of DNA Polymerase Beta in Molecular Dynamics Simulations: Improved Accuracy in Studies of Structural Features and Mutational Effects. Journal of Molecular Biology 366(2):687, doi:10.1016/j.jmb.2006.10.095.
384. V. Martinek, U. Bren, M. F. Goodman, A. Warshel, & J. Florian (2007) DNA Polymerase Beta Catalytic Efficiency Mirrors the Asn279-Dctp H-Bonding Strength. Febs Letters 581(4):775, doi:10.1016/j.febslet.2007.01.042.
383. H. Liu & A. Warshel (2007) The Catalytic Effect of Dihydrofolate Reductase and Its Mutants Is Determined by Reorganization Energies. Biochemistry 46(20):6011, doi:10.1021/bi700201w.
382. H. Liu & A. Warshel (2007) Origin of the Temperature Dependence of Isotope Effects in Enzymatic Reactions: The Case of Dihydrofolate Reductase. Journal of Physical Chemistry B 111(27):7852, doi:10.1021/jp070938f.
381. Y. Xiang, P. Oelschlaeger, J. Florian, M. F. Goodman, & A. Warshel (2006) Simulating the Effect of DNA Polymerase Mutations on Transition-State Energetics and Fidelity: Evaluating Amino Acid Group Contribution and Allosteric Coupling for Ionized Residues in Human Pol Beta. Biochemistry 45(23):7036, doi:10.1021/bi060147o.
380. A. Warshel, P. K. Sharma, M. Kato, Y. Xiang, H. Liu, & M. H. M. Olsson (2006) Electrostatic Basis for Enzyme Catalysis. Chemical Reviews 106(8):3210, doi:10.1021/cr0503106.
379. A. Warshel, P. K. Sharma, M. Kato, & W. W. Parson (2006) Modeling Electrostatic Effects in Proteins. Biochimica Et Biophysica Acta-Proteins and Proteomics 1764(11):1647, doi:10.1016/j.bbapap.2006.08.007.
376. Y. Shao, L. F. Molnar, Y. Jung, J. Kussmann, C. Ochsenfeld, S. T. Brown, A. T. B. Gilbert, L. V. Slipchenko, S. V. Levchenko, D. P. O'neill, R. A. Distasio, Jr., R. C. Lochan, T. Wang, G. J. O. Beran, N. A. Besley, J. M. Herbert, C. Y. Lin, T. Van Voorhis, S. H. Chien, A. Sodt, R. P. Steele, V. A. Rassolov, P. E. Maslen, P. P. Korambath, R. D. Adamson, B. Austin, J. Baker, E. F. C. Byrd, H. Dachsel, R. J. Doerksen, A. Dreuw, B. D. Dunietz, A. D. Dutoi, T. R. Furlani, S. R. Gwaltney, A. Heyden, S. Hirata, C.-P. Hsu, G. Kedziora, R. Z. Khalliulin, P. Klunzinger, A. M. Lee, M. S. Lee, W. Liang, I. Lotan, N. Nair, B. Peters, E. I. Proynov, P. A. Pieniazek, Y. M. Rhee, J. Ritchie, E. Rosta, C. D. Sherrill, A. C. Simmonett, J. E. Subotnik, H. L. Woodcock, Iii, W. Zhang, A. T. Bell, A. K. Chakraborty, D. M. Chipman, F. J. Keil, A. Warshel, W. J. Hehre, H. F. Schaefer, Iii, J. Kong, A. I. Krylov, P. M. W. Gill, & M. Head-Gordon (2006) Advances in Methods and Algorithms in a Modern Quantum Chemistry Program Package. Physical Chemistry Chemical Physics 8(27):3172, doi:10.1039/b517914a.
375. E. Rosta, M. Klahn, & A. Warshel (2006) Towards Accurate Ab Initio Qm/Mm Calculations of Free-Energy Profiles of Enzymatic Reactions. Journal of Physical Chemistry B 110(6):2934, doi:10.1021/jp057109j.
373. M. H. M. Olsson & A. Warshel (2006) Monte Carlo Simulations of Proton Pumps: On the Working Principles of the Biological Valve That Controls Proton Pumping in Cytochrome C Oxidase. Proceedings of the National Academy of Sciences of the United States of America 103(17):6500, doi:10.1073/pnas.0510860103.
372. M. H. M. Olsson, W. W. Parson, & A. Warshel (2006) Dynamical Contributions to Enzyme Catalysis: Critical Tests of a Popular Hypothesis. Chemical Reviews 106(5):1737, doi:10.1021/cr040427e.
371. M. H. M. Olsson, J. Mavri, & A. Warshel (2006) Transition State Theory Can Be Used in Studies of Enzyme Catalysis: Lessons from Simulations of Tunnelling and Dynamical Effects in Lipoxygenase and Other Systems. Philosophical Transactions of the Royal Society B-Biological Sciences 361(1472):1417, doi:10.1098/rstb.2006.1880.
370. J. Mavri, M. H. M. Olsson, & A. Warshel (2006) Simulation of Tunneling in Enzyme Catalysis: Application to Lipoxygenase. Recent Progress in Computational Sciences and Engineering, Vols 7a and 7b, Lecture Series on Computer and Computational Sciences, eds Simos T & Maroulis G), Vol 7A-B, pp 1113.doi.org/10.1021/ja037233l
369. M. Klaehn, E. Rosta, & A. Warshel (2006) On the Mechanism of Hydrolysis of Phosphate Monoesters Dianions in Solutions and Proteins. Journal of the American Chemical Society 128(47):15310, doi:10.1021/ja065470t.
368. M. Kato & A. Warshel (2006) Using a Charging Coordinate in Studies of Ionization Induced Partial Unfolding. Journal of Physical Chemistry B 110(23):11566, doi:10.1021/jp061190o.
367. M. Kato, A. V. Pisliakov, & A. Warshel (2006) The Barrier for Proton Transport in Aquaporins as a Challenge for Electrostatic Models: The Role of Protein Relaxation in Mutational Calculations. Proteins-Structure Function and Bioinformatics 64(4):829, doi:10.1002/prot.21012.
366. G. Hong, E. Rosta, & A. Warshel (2006) Using the Constrained Dft Approach in Generating Diabatic Surfaces and Off Diagonal Empirical Valence Bond Terms for Modeling Reactions in Condensed Phases. Journal of Physical Chemistry B 110(39):19570, doi:10.1021/jp0625199.
365. A. Burykin & A. Warshel (2006) Membranes Assembled from Narrow Carbon Nanotubes Block Proton Transport and Can Form Effective Nano-Filtration Devices. Journal of Computational and Theoretical Nanoscience 3(2):237, doi:10.1166/jctn.2006.005.
364. A. Warshel (2005) Inverting the Selectivity of Aquaporin 6: Gating Versus Direct Electrostatic Interaction. Proceedings of the National Academy of Sciences of the United States of America 102(6):1813, doi:10.1073/pnas.0409788102.
362. P. K. Sharma, Y. Xiang, M. Kato, & A. Warshel (2005) What Are the Roles of Substrate-Assisted Catalysis and Proximity Effects in Peptide Bond Formation by the Ribosome? Biochemistry 44(34):11307, doi:10.1021/bi0509806.
359. M. H. M. Olsson, P. K. Sharma, & A. Warshel (2005) Simulating Redox Coupled Proton Transfer in Cytochrome C Oxidase: Looking for the Proton Bottleneck. Febs Letters 579(10):2026, doi:10.1016/j.febslet.2005.02.051.
358. M. Klahn, S. Braun-Sand, E. Rosta, & A. Warshel (2005) On Possible Pitfalls in Ab Initio Quantum Mechanics/Molecular Mechanics Minimization Approaches for Studies of Enzymatic Reactions. Journal of Physical Chemistry B 109(32):15645, doi:10.1021/jp0521757.
356. M. Kato & A. Warshel (2005) Through the Channel and around the Channel: Validating and Comparing Microscopic Approaches for the Evaluation of Free Energy Profiles for Ion Penetration through Ion Channels. Journal of Physical Chemistry B 109(41):19516, doi:10.1021/jp0532081.
355. J. Florian, M. F. Goodman, & A. Warshel (2005) Computer Simulations of Protein Functions: Searching for the Molecular Origin of the Replication Fidelity of DNA Polymerases. Proceedings of the National Academy of Sciences of the United States of America 102(19):6819, doi:10.1073/pnas.0408173102.
354. S. Braun-Sand & A. Warshel (2005) Electrostatics of Proteins: Principles, Models and Applications pp 163, doi:10.1002/9783527619498.ch7.
352. S. Braun-Sand, M. H. M. Olsson, & A. Warshel (2005) Computer Modeling of Enzyme Catalysis and Its Relationship to Concepts in Physical Organic Chemistry. Advances in Physical Organic Chemistry, Vol 40, Advances in Physical Organic Chemistry, ed Richard JP), Vol 40, pp 201.
351. S. Braun-Sand, A. Burykin, Z. T. Chu, & A. Warshel (2005) Realistic Simulations of Proton Transport Along the Gramicidin Channel: Demonstrating the Importance of Solvation Effects. Journal of Physical Chemistry B 109(1):583, doi:10.1021/jp0465783.
348. A. Shurki & A. Warshel (2004) Why Does the Ras Switch "Break" by Oncogenic Mutations? Proteins-Structure Function and Bioinformatics 55(1):1, doi:10.1002/prot.20004.
347. A. Shurki, M. Strajbl, C. N. Schutz, & A. Warshel (2004) Electrostatic Basis for Bioenergetics. Energetics of Biological Macromolecules, Pt E 380:52.
346. C. N. Schutz & A. Warshel (2004) Analyzing Free Energy Relationships for Proton Translocations in Enzymes: Carbonic Anhydrase Revisited. Journal of Physical Chemistry B 108(6):2066, doi:10.1021/jp0366015.
345. C. N. Schutz & A. Warshel (2004) The Low Barrier Hydrogen Bond (Lbhb) Proposal Revisited: The Case of the Asp... His Pair in Serine Proteases. Proteins-Structure Function and Bioinformatics 55(3):711, doi:10.1002/prot.20096.
343. W. W. Parson & A. Warshel (2004) A Density-Matrix Model of Photosynthetic Electron Transfer with Microscopically Estimated Vibrational Relaxation Times. Chemical Physics 296(2-3):201, doi:10.1016/j.chemphys.2003.10.006.
342. W. W. Parson & A. Warshel (2004) Dependence of Photosynthetic Electron-Transfer Kinetics on Temperature and Energy in a Density-Matrix Model. Journal of Physical Chemistry B 108(29):10474, doi:10.1021/jp0495904.
340. M. H. M. Olsson & A. Warshel (2004) Solute Solvent Dynamics and Energetics in Enzyme Catalysis: The S(N)2 Reaction of Dehalogenase as a General Benchmark. Journal of the American Chemical Society 126(46):15167, doi:10.1021/ja047151c.
339. M. H. M. Olsson, P. E. M. Siegbahn, & A. Warshel (2004) Simulating Large Nuclear Quantum Mechanical Corrections in Hydrogen Atom Transfer Reactions in Metalloenzymes. Journal of Biological Inorganic Chemistry 9(1):96, doi:10.1007/s00775-003-0503-2.
338. M. H. M. Olsson, P. E. M. Siegbahn, & A. Warshel (2004) Simulations of the Large Kinetic Isotope Effect and the Temperature Dependence of the Hydrogen Atom Transfer in Lipoxygenase. Journal of the American Chemical Society 126(9):2820, doi:10.1021/ja037233l.
334. A. Burykin & A. Warshel (2004) On the Origin of the Electrostatic Barrier for Proton Transport in Aquaporin. Febs Letters 570(1-3):41, doi:10.1016/j.febslet.2004.06.020.
332. S. Braun-Sand, M. Strajbl, & A. Warshel (2004) Studies of Proton Translocations in Biological Systems: Simulating Proton Transport in Carbonic Anhydrase by Evb-Based Models. Biophysical Journal 87(4):2221, doi:10.1529/biophysj.104.043257.
331. A. Warshel & J. Villa-Freixa (2003) Comment on "Effect of Active Site Mutation Phe93 -> Trp in the Horse Liver Alcohol Dehydrogenase Enzyme on Catalysis: A Molecular Dynamics Study". Journal of Physical Chemistry B 107(44):12370, doi:10.1021/jp034932b.
330. A. Warshel (2003) Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights. Annual Review of Biophysics and Biomolecular Structure. Volume 32, Annual Review of Biophysics and Biomolecular Structure, ed Stroud RM), Vol Volume 32, pp 425.
329. A. Warshel (2003) Computer Simulations of Enzyme Catalysis: Methods, Progress, and Insights. Annual Review of Biophysics and Biomolecular Structure 32:425, doi:10.1146/annurev.biophys.32.110601.141807.
325. M. Strajbl, A. Shurki, & A. Warshel (2003) Converting Conformational Changes to Electrostatic Energy in Molecular Motors: The Energetics of Atp Synthase. Proceedings of the National Academy of Sciences of the United States of America 100(25):14834, doi:10.1073/pnas.2436328100.
324. M. Strajbl, A. Shurki, M. Kato, & A. Warshel (2003) Apparent Nac Effect in Chorismate Mutase Reflects Electrostatic Transition State Stabilization. Journal of the American Chemical Society 125(34):10228, doi:10.1021/ja0356481.
322. A. Shurki & A. Warshel (2003) Structure/Function Correlations of Proteins Using Mm, Qm/Mm, and Related Approaches: Methods, Concepts, Pitfalls, and Current Progress. Protein Simulations, Advances in Protein Chemistry, ed Daggett V), Vol 66, pp 249. doi: 10.1016/s0065-3233(03)66007-9
319. M. H. M. Olsson, G. Y. Hong, & A. Warshel (2003) Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin. Journal of the American Chemical Society 125(17):5025, doi:10.1021/ja0212157.
317. J. Florian, M. F. Goodman, & A. Warshel (2003) Computer Simulation Studies of the Fidelity of DNA Polymerases. Biopolymers 68(3):286, doi:10.1002/bip.10244.
316. J. Florian, M. F. Goodman, & A. Warshel (2003) Computer Simulation of the Chemical Catalysis of DNA Polymerases: Discriminating between Alternative Nucleotide Insertion Mechanisms for T7 DNA Polymerase. Journal of the American Chemical Society 125(27):8163, doi:10.1021/ja028997o.
315. A. Burykin & A. Warshel (2003) What Really Prevents Proton Transport through Aquaporin? Charge Self-Energy Versus Proton Wire Proposals. Biophysical Journal 85(6):3696, doi:10.1016/s0006-3495(03)74786-9.
313. A. Burykin, M. Kato, & A. Warshel (2003) Exploring the Origin of the Ion Selectivity of the Kcsa Potassium Channel. Proteins-Structure Function and Genetics 52(3):412, doi:10.1002/prot.10455.
312. M. Barbany, H. Gutierrez-De-Teran, F. Sanz, J. Villa-Freixa, & A. Warshel (2003) On the Generation of Catalytic Antibodies by Transition State Analogues. Chembiochem 4(4):277, doi:10.1002/cbic.200390048.
309. A. Warshel (2002) Molecular Dynamics Simulations of Biological Reactions. Accounts of Chemical Research 35(6):385, doi:10.1021/ar010033z.
307. M. Srajbl, G. Y. Hong, & A. Warshel (2002) Ab Initio Qm/Mm Simulation with Proper Sampling: "First Principle" Calculations of the Free Energy of the Autodissociation of Water in Aqueous Solution. Journal of Physical Chemistry B 106(51):13333, doi:10.1021/jp021625h.
305. A. Shurki, M. Strajbl, J. Villa, & A. Warshel (2002) How Much Do Enzymes Really Gain by Restraining Their Reacting Fragments? Journal of the American Chemical Society 124(15):4097, doi:10.1021/ja012230z.
302. J. Florian, A. Warshel, & M. F. Goodman (2002) Molecular Dynamics Free-Energy Simulations of the Binding Contribution to the Fidelity of T7 DNA Polymerase. Journal of Physical Chemistry B 106(22):5754, doi:10.1021/jp020791m.
299. J. Florian, M. F. Goodman, & A. Warshel (2002) Theoretical Investigation of the Binding Free Energies and Key Substrate-Recognition Components of the Replication Fidelity of Human DNA Polymerase Beta. Journal of Physical Chemistry B 106(22):5739, doi:10.1021/jp020790u.
297. A. Burykin, C. N. Schutz, J. Villa, & A. Warshel (2002) Simulations of Ion Current in Realistic Models of Ion Channels: The Kcsa Potassium Channel. Proteins-Structure Function and Genetics 47(3):265, doi:10.1002/prot.10106.
293. A. Warshel & W. W. Parson (2001) Dynamics of Biochemical and Biophysical Reactions: Insight from Computer Simulations. Quarterly Reviews of Biophysics 34(4):563, doi:10.1017/s0033583501003730.
291. A. Warshel, J. Florian, M. Strajbl, & J. Villa (2001) Circe Effect Versus Enzyme Preorganization: What Can Be Learned from the Structure of the Most Proficient Enzyme? Chembiochem 2(2):109, doi:10.1002/1439-7633(20010202)2:2<109::aid-cbic109>3.0.co;2-9.
290. A. Warshel & Z. T. Chu (2001) Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event. Journal of Physical Chemistry B 105(40):9857, doi:10.1021/jp010704a.
289. J. Villa & A. Warshel (2001) Energetics and Dynamics of Enzymatic Reactions. Journal of Physical Chemistry B 105(33):7887, doi:10.1021/jp011048h.
288. M. Strajbl, J. Florian, & A. Warshel (2001) Ab Initio Evaluation of the Free Energy Surfaces for the General Base/acid Catalyzed Thiolysis of Formamide and the Hydrolysis of Methyl Thiolformate: A Reference Solution Reaction for Studies of Cysteine Proteases. Journal of Physical Chemistry B 105(19):4471, doi:10.1021/jp010279l.
287. C. N. Schutz & A. Warshel (2001) What Are the Dielectric "Constants" of Proteins and How to Validate Electrostatic Models? Proteins-Structure Function and Genetics 44(4):400, doi:10.1002/prot.1106.
286. A. Warshel, M. Strajbl, J. Villa, & J. Florian (2000) Remarkable Rate Enhancement of Orotidine 5 '-Monophosphate Decarboxylase Is Due to Transition-State Stabilization Rather Than to Ground-State Destabilization. Biochemistry 39(48):14728, doi:10.1021/bi000987h.
285. A. Warshel, Y. Y. Sham, & I. Muegge (2000) Simulating Proton Translocations in Proteins: Probing Proton Transfer Pathways in the Rhodobacter Sphaeroides Reaction Center. European Biophysics Journal 29(4-5):237.
283. A. Warshel (2000) Perspective on "the Energetics of Enzymatic Reactions" - Warshel a (1978) Proc Natl Acad Sci USA 75 : 5250. Theoretical Chemistry Accounts 103(3-4):337, doi:10.1007/s002149900047.
281. J. Villa, M. Strajbl, T. M. Glennon, Y. Y. Sham, Z. T. Chu, & A. Warshel (2000) How Important Are Entropic Contributions to Enzyme Catalysis? Proceedings of the National Academy of Sciences of the United States of America 97(22):11899, doi:10.1073/pnas.97.22.11899.
280. J. Villa, J. Bentzien, A. Gonzalez-Lafont, J. M. Lluch, J. Bertran, & A. Warshel (2000) Effective Way of Modeling Chemical Catalysis: Empirical Valence Bond Picture of Role of Solvent and Catalyst in Alkylation Reactions. Journal of Computational Chemistry 21(8):607, doi:10.1002/(sici)1096-987x(200006)21:8<607::aid-jcc3>3.0.co;2-r.
279. P. Varnai & A. Warshel (2000) Computer Simulation Studies of the Catalytic Mechanism of Human Aldose Reductase. Journal of the American Chemical Society 122(16):3849, doi:10.1021/ja994246j.
278. P. Varnai, P. D. Lyne, A. Warshel, & W. G. Richards (2000) Is Human Aldose Reductase an Effective Catalyst? Journal of Molecular Graphics and Modelling 18(2):216.
277. M. Strajbl, Y. Y. Sham, J. Villa, Z. T. Chu, & A. Warshel (2000) Calculations of Activation Entropies of Chemical Reactions in Solution. Journal of Physical Chemistry B 104(18):4578, doi:10.1021/jp0003095.
276. M. Strajbl, J. Florian, & A. Warshel (2000) Ab Initio/Ld Studies of Chemical Reactions in Solution: Reference Free-Energy Surfaces for Acylation Reactions Occurring in Serine and Cysteine Proteases. International Journal of Quantum Chemistry 77(1):44, doi:10.1002/(sici)1097-461x(2000)77:1<44::aid-qua6>3.0.co;2-a.
275. M. Strajbl, J. Florian, & A. Warshel (2000) Ab Initio Evaluation of the Potential Surface for General Base-Catalyzed Methanolysis of Formamide: A Reference Solution Reaction for Studies of Serine Proteases. Journal of the American Chemical Society 122(22):5354, doi:10.1021/ja992441s.
273. Y. Y. Sham, Z. T. Chu, H. Tao, & A. Warshel (2000) Examining Methods for Calculations of Binding Free Energies: Lra, Lie, Pdld-Lra, and Pdld/S-Lra Calculations of Ligands Binding to an Hiv Protease. Proteins-Structure Function and Genetics 39(4):393, doi:10.1002/(sici)1097-0134(20000601)39:4<393::aid-prot120>3.0.co;2-h.
272. E. L. Mehler & A. Warshel (2000) Comment on "a Fast and Simple Method to Calculate Protonation States in Proteins". Proteins-Structure Function and Genetics 40(1):1.
271. J. Kong, C. A. White, A. I. Krylov, D. Sherrill, R. D. Adamson, T. R. Furlani, M. S. Lee, A. M. Lee, S. R. Gwaltney, T. R. Adams, C. Ochsenfeld, A. T. B. Gilbert, G. S. Kedziora, V. A. Rassolov, D. R. Maurice, N. Nair, Y. H. Shao, N. A. Besley, P. E. Maslen, J. P. Dombroski, H. Daschel, W. M. Zhang, P. P. Korambath, J. Baker, E. F. C. Byrd, T. Van Voorhis, M. Oumi, S. Hirata, C. P. Hsu, N. Ishikawa, J. Florian, A. Warshel, B. G. Johnson, P. M. W. Gill, M. Head-Gordon, & J. A. Pople (2000) Q-Chem 2.0: A High-Performance Ab Initio Electronic Structure Program Package. Journal of Computational Chemistry 21(16):1532, doi:10.1002/1096-987x(200012)21:16<1532::aid-jcc10>3.0.co;2-w.
269. G. Y. Hong, M. Strajbl, T. A. Wesolowski, & A. Warshel (2000) Constraining the Electron Densities in Dft Method as an Effective Way for Ab Initio Studies of Metal-Catalyzed Reactions. Journal of Computational Chemistry 21(16):1554, doi:10.1002/1096-987x(200012)21:16<1554::aid-jcc12>3.0.co;2-i.
268. T. M. Glennon, J. Villa, & A. Warshel (2000) How Does Gap Catalyze the Gtpase Reaction of Ras?: A Computer Simulation Study. Biochemistry 39(32):9641, doi:10.1021/bi000640e.
267. J. Florian, M. F. Goodman, & A. Warshel (2000) Free-Energy Perturbation Calculations of DNA Destabilization by Base Substitutions: The Effect of Neutral Guanine Thymine, Adenine Cytosine and Adenine Difluorotoluene Mismatches. Journal of Physical Chemistry B 104(43):10092, doi:10.1021/jp001760z.
263. Y. Y. Sham, I. Muegge, & A. Warshel (1999) Simulating Proton Translocations in Proteins: Probing Proton Transfer Pathways in the Rhodobacter Sphaeroides Reaction Center. Proteins-Structure Function and Bioinformatics 36(4):484.
262. L. A. Jenkins, J. K. Bashkin, J. D. Pennock, J. Florian, & A. Warshel (1999) Catalytic Hydrolysis of Adenosine 2 ',3 '-Cyclic Monophosphate by Cu(Ii) Terpyridine. Inorganic Chemistry 38(13):3215, doi:10.1021/ic990228r.
261. C. F. Jen & A. Warshel (1999) Microscopic Based Density Matrix Treatments of Electron-Transfer Reactions in Condensed Phases. Journal of Physical Chemistry A 103(51):11378, doi:10.1021/jp991304e.
259. M. Fuxreiter, A. Warshel, & R. Osman (1999) Role of Active Site Residues in the Glycosylase Step of T4 Endonuclease V. Computer Simulation Studies on Ionization States. Biochemistry 38(30):9577, doi:10.1021/bi9901937.
258. J. Florian & A. Warshel (1999) Quantum-Chemical Insights into Mechanisms of the Nonenzymatic Hydrolysis of Phosphate Monoesters. Phosphorus Sulfur and Silicon and the Related Elements 146:525.
257. J. Florian & A. Warshel (1999) Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Langevin Dipoles Solvation Model. Journal of Physical Chemistry B 103(46):10282, doi:10.1021/jp992041r.
256. J. Florian, J. Sponer, & A. Warshel (1999) Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution: Ab Initio/Langevin Dipoles Study. Journal of Physical Chemistry B 103(5):884, doi:10.1021/jp983699s.
255. Z. Z. Fan, J. K. Hwang, & A. Warshel (1999) Using Simplified Protein Representation as a Reference Potential for All-Atom Calculations of Folding Free Energy. Theoretical Chemistry Accounts 103(1):77, doi:10.1007/s002140050516.
254. J. Aqvist, K. Kolmodin, J. Florian, & A. Warshel (1999) Mechanistic Alternatives Phosphate Monoester Hydrolysis: What Conclusions Can Be Drawn from Available Experimental Data? Chemistry & Biology 6(3):R71, doi:10.1016/s1074-5521(99)89003-6.
253. A. Warshel & A. Papazyan (1998) Electrostatic Effects in Macromolecules: Fundamental Concepts and Practical Modeling. Current Opinion in Structural Biology 8(2):211, doi:10.1016/s0959-440x(98)80041-9.
252. A. Warshel & J. Florian (1998) Computer Simulations of Enzyme Catalysis: Finding out What Has Been Optimized by Evolution. Proceedings of the National Academy of Sciences of the United States of America 95(11):5950, doi:10.1073/pnas.95.11.5950.
248. A. Warshel (1998) Electrostatic Origin of the Catalytic Power of Enzymes and the Role of Preorganized Active Sites. Journal of Biological Chemistry 273(42):27035, doi:10.1074/jbc.273.42.27035.
247. Y. Y. Sham & A. Warshel (1998) The Surface Constraint All Atom Model Provides Size Independent Results in Calculations of Hydration Free Energies. Journal of Chemical Physics 109(18):7940, doi:10.1063/1.477441.
245. W. W. Parson, Z. T. Chu, & A. Warshel (1998) Free Energy Functions for Charge Separation in Wild-Type and Mutant Bacterial Reaction Centers pp 703.
243. W. W. Parson, Z. T. Chu, & A. Warshel (1998) Oscillations of the Energy Gap for the Initial Electron-Transfer Step in Bacterial Reaction Centers. Photosynthesis Research 55(2-3):147, doi:10.1023/a:1005992121305.
242. A. Papazyan & A. Warshel (1998) Effect of Solvent Discreteness on Solvation. Journal of Physical Chemistry B 102(27):5348, doi:10.1021/jp981725g.
241. I. Muegge, T. Schweins, & A. Warshel (1998) Electrostatic Contributions to Protein-Protein Binding Affinities: Application to Rap/Raf Interaction. Proteins-Structure Function and Genetics 30(4):407, doi:10.1002/(sici)1097-0134(19980301)30:4<407::aid-prot8>3.0.co;2-f.
240. G. M. Jensen, S. W. Bunte, A. Warshel, & D. B. Goodin (1998) Energetics of Cation Radical Formation at the Proximal Active Site Tryptophan of Cytochrome C Peroxidase and Ascorbate Peroxidase. Journal of Physical Chemistry B 102(42):8221, doi:10.1021/jp9811326.
239. T. M. Glennon & A. Warshel (1998) Energetics of the Catalytic Reaction of Ribonuclease A: A Computational Study of Alternative Mechanisms. Journal of the American Chemical Society 120(39):10234, doi:10.1021/ja981594x.
238. M. Fuxreiter & A. Warshel (1998) Origin of the Catalytic Power of Acetylcholinesterase: Computer Simulation Studies. Journal of the American Chemical Society 120(1):183, doi:10.1021/ja972326m.
237. J. Florian & A. Warshel (1998) Phosphate Ester Hydrolysis in Aqueous Solution: Associative Versus Dissociative Mechanisms. Journal of Physical Chemistry B 102(4):719, doi:10.1021/jp972182y.
236. J. Florian, M. Strajbl, & A. Warshel (1998) Conformational Flexibility of Phosphate, Phosphonate, and Phosphorothioate Methyl Esters in Aqueous Solution. Journal of the American Chemical Society 120(31):7959, doi:10.1021/ja9710823.
235. J. Florian, J. Aqvist, & A. Warshel (1998) On the Reactivity of Phosphate Monoester Dianions in Aqueous Solution: Bronsted Linear Free-Energy Relationships Do Not Have an Unique Mechanistic Interpretation. Journal of the American Chemical Society 120(44):11524, doi:10.1021/ja982698a.
234. J. Bentzien, R. P. Muller, J. Florian, & A. Warshel (1998) Hybrid Ab Initio Quantum Mechanics Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin. Journal of Physical Chemistry B 102(12):2293, doi:10.1021/jp973480y.
233. A. Warshel, A. Papazyan, & I. Muegge (1997) Microscopic and Semimacroscopic Redox Calculations: What Can and Cannot Be Learned from Continuum Models. Journal of Biological Inorganic Chemistry 2(1):143, doi:10.1007/s007750050119.
232. A. Warshel, Z. T. Chu, & W. W. Parson (1997) Two-Dimensional Free Energy Surfaces for Primary Electron Transfer in a Photosynthetic Reaction Center. Chemical Physics Letters 265(1-2):293, doi:10.1016/s0009-2614(96)01415-7.
231. A. Warshel (1997) Computer Simulations of the Action of Metalloenzymes pp 343.
228. J. Tomasi, B. Mennucci, R. Cammi, & M. Cossi (1997) Quantum Mechanical Models for Reactions in Solution pp 1.
227. R. H. Stote, A. Dejaegere, & M. Karplus (1997) Molecular Mechanics and Dynamics Simulations of Enzymes pp 153.
226. R. V. Stanton, S. L. Dixon, & K. M. Merz, Jr. (1997) Free Energy Perturbation Calculations within Quantum Mechanical Methodologies pp 103.
225. K. A. Sharp (1997) Electrostatic Interactions in Proteins pp 199.
224. Y. Y. Sham, Z. T. Chu, & A. Warshel (1997) Consistent Calculations of Pk(a)'S of Ionizable Residues in Proteins: Semi-Microscopic and Microscopic Approaches. Journal of Physical Chemistry B 101(22):4458, doi:10.1021/jp963412w.
223. A. Papazyan & A. Warshel (1997) A Stringent Test of the Cavity Concept in Continuum Dielectrics. Journal of Chemical Physics 107(19):7975, doi:10.1063/1.475059.
222. A. Papazyan & A. Warshel (1997) Continuum and Dipole-Lattice Models of Solvation. Journal of Physical Chemistry B 101(51):11254, doi:10.1021/jp971632j.
221. G. Naray-Szabo, M. Fuxreiter, & A. Warshel (1997) Electrostatic Basis of Enzyme Catalysis pp 237.
220. R. P. Muller, T. Wesolowski, & A. Warshel (1997) Calculations of Chemical Processes in Solution by Density-Functional and Other Quantum-Mechanical Techniques. Density-Functional Methods in Chemistry and Materials Science:189.
219. R. P. Muller, J. Florian, & A. Warshel (1997) Semiempirical and Ab Initio Modeling of Chemical Processes - from Aqueous Solution to Enzymes. Biomolecular Structure and Dynamics, Nato Advanced Science Institutes Series, Series E, Applied Sciences, eds Vergoten G & Theophanides T), Vol 342, pp 47.
218. I. Muegge, H. Tao, & A. Warshel (1997) A Fast Estimate of Electrostatic Group Contributions to the Free Energy of Protein-Inhibitor Binding. Protein Engineering 10(12):1363, doi:10.1093/protein/10.12.1363.
217. I. Muegge, P. X. Qi, A. J. Wand, Z. T. Chu, & A. Warshel (1997) The Reorganization Energy of Cytochrome C Revisited. Journal of Physical Chemistry B 101(5):825, doi:10.1021/jp962478o.
216. T. P. Lybrand (1997) Protein-Ligand Interactions pp 363.
215. J. K. Hwang & A. Warshel (1997) On the Relationship between the Dispersed Polaron and Spin-Boson Models. Chemical Physics Letters 271(4-6):223, doi:10.1016/s0009-2614(97)00482-x.
214. A. Goldblum (1997) On the Mechanisms of Proteinases pp 295.
213. J. Florian & A. Warshel (1997) A Fundamental Assumption About Oh- Attack in Phosphate Ester Hydrolysis Is Not Fully Justified. Journal of the American Chemical Society 119(23):5473, doi:10.1021/ja964270m.
212. J. Florian & A. Warshel (1997) Langevin Dipoles Model for Ab Initio Calculations of Chemical Processes in Solution: Parametrization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution. Journal of Physical Chemistry B 101(28):5583, doi:10.1021/jp9705075.
210. M. J. Field (1997) Hybrid Potentials for Molecular Systems in the Condensed Phase pp 125.
208. J. Avist (1997) Modelling of Proton Transfer Reactions in Enzymes pp 341.
207. Anonymous (1997) Understanding Chemical Reactivity, Vol. 19; Computational Approaches to Biochemical Reactivity pp x+379p.
206. T. Wesolowski, R. P. Muller, & A. Warshel (1996) Ab Initio Frozen Density Functional Calculations of Proton Transfer Reactions in Solution. Journal of Physical Chemistry 100(38):15444, doi:10.1021/jp961068x.
205. A. Warshel & A. Papazyan (1996) Energy Considerations Show That Low-Barrier Hydrogen Bonds Do Not Offer a Catalytic Advantage over Ordinary Hydrogen Bonds. Proceedings of the National Academy of Sciences of the United States of America 93(24):13665, doi:10.1073/pnas.93.24.13665.
202. P. J. Stephens, D. R. Jollie, & A. Warshel (1996) Protein Control of Redox Potentials of Iron-Sulfur Proteins. Chemical Reviews 96(7):2491, doi:10.1021/cr950045w.
201. T. Schweins & A. Warshel (1996) Mechanistic Analysis of the Observed Linear Free Energy Relationships in P21(Ras) and Related Systems. Biochemistry 35(45):14232, doi:10.1021/bi961119g.
200. T. Schweins, M. Geyer, H. R. Kalbitzer, A. Wittinghofer, & A. Warshel (1996) Linear Free Energy Relationships in the Intrinsic and Gtpase Activating Protein-Stimulated Guanosine 5'-Triphosphate Hydrolysis of P21(Ras). Biochemistry 35(45):14225, doi:10.1021/bi961118o.
199. I. Muegge, T. Schweins, R. Langen, & A. Warshel (1996) Electrostatic Control of Gtp and Gdp Binding in the Oncoprotein P21(Ras). Structure 4(4):475, doi:10.1016/s0969-2126(96)00052-4.
198. J. D. Madura, Y. Nakajima, R. M. Hamilton, A. Wierzbicki, & A. Warshel (1996) Calculations of the Electrostatic Free Energy Contributions to the Binding Free Energy of Sulfonamides to Carbonic Anhydrase. Structural Chemistry 7(2):131, doi:10.1007/bf02278738.
197. J. K. Hwang & A. Warshel (1996) How Important Are Quantum Mechanical Nuclear Motions in Enzyme Catalysis? Journal of the American Chemical Society 118(47):11745, doi:10.1021/ja962007f.
195. R. G. Alden, W. W. Parson, Z. T. Chu, & A. Warshel (1996) Orientation of the Oh Dipole of Tyrosine (M)210 and Its Effect on Electrostatic Energies in Photosynthetic Bacterial Reaction Centers. Journal of Physical Chemistry 100(41):16761, doi:10.1021/jp961271s.
194. A. Warshel, A. Papazyan, & P. A. Kollman (1995) On Low-Barrier Hydrogen-Bonds and Enzyme Catalysis. Science 269(5220):102, doi:10.1126/science.7661987.
192. T. Schweins, M. Geyer, K. Scheffzek, A. Warshel, H. R. Kalbitzer, & A. Wittinghofer (1995) Substrate-Assisted Catalysis as a Mechanism for Gtp Hydrolysis of P21(Ras) and Other Gtp-Binding Proteins. Nature Structural Biology 2(1):36, doi:10.1038/nsb0195-36.
190. R. P. Muller & A. Warshel (1995) Ab-Initio Calculations of Free-Energy Barriers for Chemical-Reactions in Solution. Journal of Physical Chemistry 99(49):17516, doi:10.1021/j100049a009.
189. Y. S. Kong & A. Warshel (1995) Linear Free-Energy Relationships with Quantum-Mechanical Corrections - Classical and Quantum-Mechanical Rate Constants for Hydride Transfer between Nad(+) Analogs in Solutions. Journal of the American Chemical Society 117(23):6234, doi:10.1021/ja00128a009.
188. M. Fothergill, M. F. Goodman, J. Petruska, & A. Warshel (1995) Structure-Energy Analysis of the Role of Metal-Ions in Phosphodiester Bond Hydrolysis by DNA-Polymerase-I. Journal of the American Chemical Society 117(47):11619, doi:10.1021/ja00152a001.
187. R. G. Alden, W. W. Parson, Z. T. Chu, & A. Warshel (1995) Calculations of Electrostatic Energies in Photosynthetic Reaction Centers. Journal of the American Chemical Society 117(49):12284, doi:10.1021/ja00154a031.
186. T. Wesolowski & A. Warshel (1994) Ab-Initio Free-Energy Perturbation Calculations of Solvation Free-Energy Using the Frozen Density-Functional Approach. Journal of Physical Chemistry 98(20):5183, doi:10.1021/j100071a003.
185. A. Warshel, H. Tao, M. Fothergill, & Z. T. Chu (1994) Effective Methods for Estimation of Binding-Energies in Computer-Aided Drug Design. Israel Journal of Chemistry 34(2):253.
184. A. Warshel, T. Schweins, & M. Fothergill (1994) Linear Free-Energy Relationships in Enzymes - Theoretical-Analysis of the Reaction of Tyrosyl-Transfer-Rna Synthetase. Journal of the American Chemical Society 116(19):8437, doi:10.1021/ja00098a001.
183. A. Warshel, Z. T. Chu, & W. W. Parson (1994) On the Energetics of the Primary Electron-Transfer Process in Bacterial Reaction Centers. Journal of Photochemistry and Photobiology a-Chemistry 82(1-3):123, doi:10.1016/1010-6030(94)02010-8.
182. A. Warshel & Z. T. Chu (1994) Calculations of Solvation Free-Energies in Chemistry and Biology. Structure and Reactivity in Aqueous Solution: Characterization of Chemical and Biological Systems, Acs Symposium Series, eds Cramer CJ & Truhlar DG), Vol 568, pp 71.
179. T. Schweins, K. Scheffzek, A. Warshel, M. Geyer, H. R. Kalbitzer, & F. Wittinghofer (1994) Structural and Biochemical Studies on the P21-Ras Catalyzed Gtpase and Its Stimulation by Gap. FASEB Journal 8(7):A1430.
178. T. Schweins, K. Scheffzek, A. Warshel, M. Geyer, H. R. Kalbitzer, & F. Wittinghofer (1994) Structural and Biochemical-Studies on the P21(Ras) Catalyzed Gtpase and Its Stimulation by Gap. FASEB Journal 8(7):A1430.
177. T. Schweins, R. Langen, & A. Warshel (1994) Why Have Mutagenesis Studies Not Located the General Base in Ras P21. Nature Structural Biology 1(7):476, doi:10.1038/nsb0794-476.
176. T. Schweins, M. Geyer, K. Scheffzek, H. R. Kalbitzer, A. Warshel, & A. Wittinghofer (1994) A Novel Reaction Mechanism for the Gtpase of Ras-P21. Biological Chemistry Hoppe-Seyler 375(SPEC. SUPPL. 1):S94.
175. G. M. Jensen, A. Warshel, & P. J. Stephens (1994) Calculation of the Redox Potentials of Iron-Sulfur Proteins - the 2-/3--Couple of Fe4s4-Asterisk-Cys(4) Clusters in Peptococcus-Aerogenes Ferredoxin, Azotobacter-Vinelandii Ferredoxin-I, and Chromatium-Vinosum High-Potential Iron Protein. Biochemistry 33(36):10911, doi:10.1021/bi00202a010.
174. R. Alden, V. Nagarajan, W. Parson, C. Schenck, & A. Warshel (1994) Theoretical and Experimental Studies of the Initial Electron-Transfer Step in Bacterial Reaction Centers. Photochemistry and Photobiology 59(SPEC. ISSUE):53S.
173. T. A. Wesolowski & A. Warshel (1993) Frozen Density-Functional Approach for Ab-Initio Calculations of Solvated Molecules. Journal of Physical Chemistry 97(30):8050, doi:10.1021/j100132a040.
170. J. G. Pearson, E. Oldfield, F. S. Lee, & A. Warshel (1993) Chemical-Shifts in Proteins - a Shielding Trajectory Analysis of the Fluorine Nuclear-Magnetic-Resonance Spectrum of the Escherichia-Coli Galactose Binding-Protein Using a Multipole Shielding Polarizability Local Reaction Field Molecular-Dynamics Approach. Journal of the American Chemical Society 115(15):6851, doi:10.1021/ja00068a049.
169. F. S. Lee, Z. T. Chu, & A. Warshel (1993) Microscopic and Semimicroscopic Calculations of Electrostatic Energies in Proteins by the Polaris and Enzymix Programs. Journal of Computational Chemistry 14(2):161, doi:10.1002/jcc.540140205.
168. J. K. Hwang & A. Warshel (1993) A Quantized Classical Path Approach for Calculations of Quantum-Mechanical Rate Constants. Journal of Physical Chemistry 97(39):10053, doi:10.1021/j100141a026.
167. J. Aqvist & A. Warshel (1993) Molecular Recognition in the Catalytic Action of Metallo-Enzymes pp 108.
166. J. Aqvist & A. Warshel (1993) Simulation of Enzyme-Reactions Using Valence-Bond Force-Fields and Other Hybrid Quantum-Classical Approaches. Chemical Reviews 93(7):2523.
165. J. Aqvist, M. Fothergill, & A. Warshel (1993) Computer-Simulation of the Co2/Hco3- Interconversion Step in Human Carbonic Anhydrase-I. Journal of the American Chemical Society 115(2):631.
163. A. Warshel, J. K. Hwang, & Z. T. Chu (1992) Simulations of Quantum Dynamics in Proton-Transfer and Hydrid Transfer-Reactions in Proteins. FASEB Journal 6(1):A277.
162. A. Warshel, J. K. Hwang, & J. Aqvist (1992) Computer Simulations of Enzymatic Reactions: Examination of Linear Free-Energy Relationships and Quantum-Mechanical Corrections in the Initial Proton-Transfer Step of Carbonic Anhydrase. Faraday Discussions; Structure and Activity of Enzymes, Faraday Discussions, ed Sarre PJ), Vol 93, pp 225.
161. A. Warshel, J. K. Hwang, & J. Aqvist (1992) Computer-Simulations of Enzymatic-Reactions - Examination of Linear Free-Energy Relationships and Quantum-Mechanical Corrections in the Initial Proton-Transfer Step of Carbonic-Anhydrase. Faraday Discussions 93:225, doi:10.1039/fd9929300225.
160. A. Warshel (1992) Simulations of Proton-Transfer and Hydride Transfer-Reactions in Proteins pp 175.
159. A. Warshel (1992) Computer-Simulations of Charge Separation Processes in Model Compounds and Bacterial Reaction Centers. Photosynthesis Research 34(1):91.
158. N. Vaidehi, T. A. Wesolowski, & A. Warshel (1992) Quantum-Mechanical Calculations of Solvation Free-Energies - a Combined Abinitio Pseudopotential Free-Energy Perturbation Approach. Journal of Chemical Physics 97(6):4264, doi:10.1063/1.463928.
157. V. Luzhkov & A. Warshel (1992) Microscopic Models for Quantum-Mechanical Calculations of Chemical Processes in Solutions - Ld/ampac and Scaas/ampac Calculations of Solvation Energies. Journal of Computational Chemistry 13(2):199, doi:10.1002/jcc.540130212.
156. F. S. Lee & A. Warshel (1992) A Local Reaction Field Method for Fast Evaluation of Long-Range Electrostatic Interactions in Molecular Simulations. Journal of Chemical Physics 97(5):3100, doi:10.1063/1.462997.
155. F. S. Lee, Z. T. Chu, M. B. Bolger, & A. Warshel (1992) Calculations of Antibody Antigen Interactions - Microscopic and Semimicroscopic Evaluation of the Free-Energies of Binding of Phosphorylcholine Analogs to Mcpc603. Protein Engineering 5(3):215, doi:10.1093/protein/5.3.215.
154. R. Langen, T. Schweins, & A. Warshel (1992) On the Mechanism of Guanosine Triphosphate Hydrolysis in Ras P21 Proteins. Biochemistry 31(37):8691, doi:10.1021/bi00152a002.
153. R. Langen, G. M. Jensen, U. Jacob, P. J. Stephens, & A. Warshel (1992) Protein Control of Iron-Sulfur Cluster Redox Potentials. Journal of Biological Chemistry 267(36):25625.
152. R. Langen, G. D. Brayer, A. M. Berghuis, G. Mclendon, F. Sherman, & A. Warshel (1992) Effect of the Asn52- Ile Mutation on the Redox Potential of Yeast Cytochrome-C - Theory and Experiment. Journal of Molecular Biology 224(3):589, doi:10.1016/0022-2836(92)90546-v.
151. J. Aqvist & A. Warshel (1992) Computer-Simulation of the Initial Proton-Transfer Step in Human Carbonic Anhydrase-I. Journal of Molecular Biology 224(1):7.
150. A. Yadav, R. M. Jackson, J. J. Holbrook, & A. Warshel (1991) Role of Solvent Reorganization Energies in the Catalytic Activity of Enzymes. Journal of the American Chemical Society 113(13):4800, doi:10.1021/ja00013a013.
149. A. Warshel & W. W. Parson (1991) Computer-Simulations of Electron-Transfer Reactions in Solution and in Photosynthetic Reaction Centers. Annual Review of Physical Chemistry 42:279, doi:10.1146/annurev.physchem.42.1.279.
148. A. Warshel, Z. T. Chu, & J. K. Hwang (1991) The Dynamics of the Primary Event in Rhodopsins Revisited. Chemical Physics 158(2-3):303, doi:10.1016/0301-0104(91)87074-6.
147. A. Warshel & J. Aqvist (1991) Electrostatic Energy and Macromolecular Function. Engelman, D. M., Annual Review of Biophysics and Biophysical Chemistry), pp 267.
146. A. Warshel & J. Aqvist (1991) Microscopic Simulations of Chemical Processes in Proteins and the Role of Electrostatic Free Energy pp 257.
145. A. Warshel & J. Aqvist (1991) Electrostatic Energy and Macromolecular Function. Annual Review of Biophysics and Biophysical Chemistry 20:267, doi:10.1146/annurev.bb.20.060191.001411.
142. V. Luzhkov & A. Warshel (1991) Microscopic Calculations of Solvent Effects on Absorption-Spectra of Conjugated Molecules. Journal of the American Chemical Society 113(12):4491, doi:10.1021/ja00012a018.
141. G. King, F. S. Lee, & A. Warshel (1991) Microscopic Simulations of Macroscopic Dielectric-Constants of Solvated Proteins. Journal of Chemical Physics 95(6):4366, doi:10.1063/1.461760.
140. J. K. Hwang, Z. T. Chu, A. Yadav, & A. Warshel (1991) Simulations of Quantum-Mechanical Corrections for Rate Constants of Hydride-Transfer Reactions in Enzymes and Solutions. Journal of Physical Chemistry 95(22):8445, doi:10.1021/j100175a009.
139. J. Aqvist, H. Luecke, F. A. Quiocho, & A. Warshel (1991) Dipoles Localized at Helix Termini of Proteins Stabilize Charges. Proceedings of the National Academy of Sciences of the United States of America 88(5):2026, doi:10.1073/pnas.88.5.2026.
138. A. Warshel & Z. T. Chu (1990) Quantum Corrections for Rate Constants of Diabatic and Adiabatic Reactions in Solutions. Journal of Chemical Physics 93(6):4003, doi:10.1063/1.458785.
137. A. Warshel (1990) Computer Aided Enzyme Design. Protein Engineering 3(4):281.
136. A. Warshel (1990) Electrostatic Free-Energy as the Fundamental Structure-Function Correlator in Proteins - Some Perspectives from Microscopic Simulations of Proteins Functions pp 515.
134. W. Pason, V. Nagarajan, Z. Chu, A. Warshel, D. Gaul, & C. Schenck (1990) Mechanism of the Inital Electron Transfer Step in Bacterial Photosynthesis. Photochemistry and Photobiology 51(SUPPL):80S.
133. W. W. Parson, S. Creighton, Z. T. Chu, & A. Warshel (1990) Primary Electron-Transfer Mechanisms in Bacterial Reaction Centers pp A31.
132. W. W. Parson, Z. T. Chu, & A. Warshel (1990) Electrostatic Control of Charge Separation in Bacterial Photosynthesis. Biochimica Et Biophysica Acta 1017(3):251, doi:10.1016/0005-2728(90)90192-7.
131. S. Kuwajima & A. Warshel (1990) Incorporating Electric Polarizabilities in Water Water Interaction Potentials. Journal of Physical Chemistry 94(1):460, doi:10.1021/j100364a080.
130. G. King & A. Warshel (1990) Investigation of the Free-Energy Functions for Electron-Transfer Reactions. Journal of Chemical Physics 93(12):8682, doi:10.1063/1.459255.
129. J. Aqvist & A. Warshel (1990) Free-Energy Relationships in Metalloenzyme-Catalyzed Reactions - Calculations of the Effects of Metal-Ion Substitutions in Staphylococcal Nuclease. Journal of the American Chemical Society 112(8):2860.
128. A. Warshel, G. Narayszabo, F. Sussman, & J. K. Hwang (1989) How Do Serine Proteases Really Work. Biochemistry 28(9):3629, doi:10.1021/bi00435a001.
127. A. Warshel, Z. T. Chu, & W. W. Parson (1989) Dispersed Polaron Simulations of Electron-Transfer in Photosynthetic Reaction Centers. Science 246(4926):112, doi:10.1126/science.2675313.
126. A. Warshel, J. Aqvist, & S. Creighton (1989) Enzymes Work by Solvation Substitution Rather Than by Desolvation. Proceedings of the National Academy of Sciences of the United States of America 86(15):5820, doi:10.1073/pnas.86.15.5820.
125. A. Warshel & J. Aqvist (1989) Electrostatic Correlation of Structure and Function in Proteins. Chemica Scripta 29A:75.
124. A. Warshel (1989) Exploring Enzyme Catalytic Mechanism by Cad Approaches. Journal of Cellular Biochemistry Supplement (13 PART A):15.
123. A. Warshel (1989) Microscopic Simulations of Chemical-Reactions in Solutions and Protein Active-Sites - Principles and Examples pp 305.
121. W. W. Parson, S. Creighton, & A. Warshel (1989) Calculations of Charge-Transfer Transition Energies and Spectroscopic Properties of a Molecular-Crystal - Methylbacteriopheophorbide-A. Journal of the American Chemical Society 111(12):4277, doi:10.1021/ja00194a019.
120. G. Narayszabo & A. Warshel (1989) Electrostatics and Protein Engineering pp 169.
119. G. King & A. Warshel (1989) A Surface Constrained All-Atom Solvent Model for Effective Simulations of Polar Solutions. Journal of Chemical Physics 91(6):3647, doi:10.1063/1.456845.
118. R. L. Cutler, A. M. Davies, S. Creighton, A. Warshel, G. R. Moore, M. Smith, & A. G. Mauk (1989) Role of Arginine-38 in Regulation of the Cytochrome-C Oxidation-Reduction Equilibrium. Biochemistry 28(8):3188, doi:10.1021/bi00434a012.
117. Z. T. Chu, A. Warshel, & W. W. Parson (1989) Microscopic Simulation of Quantum Dynamics and Nuclear Tunneling in Bacterial Reaction Centers. Photosynthesis Research 22(1):39, doi:10.1007/bf00114765.
116. M. B. Bolger, J. K. Hwang, S. Creighton, & A. Warshel (1989) Molecular Modeling and Free Energy Calculations on Antibody Variable Regions. Journal of Cellular Biochemistry Supplement (13 PART A):83.
115. J. Aqvist & A. Warshel (1989) Calculations of Free-Energy Profiles for the Staphylococcal Nuclease Catalyzed Reaction. Biochemistry 28(11):4680.
113. A. Warshel, F. Sussman, & J. K. Hwang (1988) Evaluation of Catalytic Free-Energies in Genetically Modified Proteins. Journal of Molecular Biology 201(1):139, doi:10.1016/0022-2836(88)90445-7.
112. A. Warshel, S. Creighton, & W. W. Parson (1988) Electron-Transfer Pathways in the Primary Event of Bacterial Photosynthesis. Journal of Physical Chemistry 92(9):2696, doi:10.1021/j100320a057.
110. S. Kuwajima & A. Warshel (1988) The Extended Ewald Method - a General Treatment of Long-Range Electrostatic Interactions in Microscopic Simulations. Journal of Chemical Physics 89(6):3751, doi:10.1063/1.454897.
109. J. K. Hwang & A. Warshel (1988) Why Ion-Pair Reversal by Protein Engineering Is Unlikely to Succeed. Nature 334(6179):270, doi:10.1038/334270a0.
108. J. K. Hwang, F. Sussman, & A. Warshel (1988) Simulating the Energetics and Dynamics of Enzymatic Reaction in Genetically Modified Subtilisin pp 95.
107. J. K. Hwang, G. King, S. Creighton, & A. Warshel (1988) Simulation of Free-Energy Relationships and Dynamics of Sn2 Reactions in Aqueous-Solution. Journal of the American Chemical Society 110(16):5297, doi:10.1021/ja00224a011.
106. J. K. Hwang, S. Creighton, G. King, D. Whitney, & A. Warshel (1988) Effects of Solute Solvent Coupling and Solvent Saturation on Solvation Dynamics of Charge-Transfer Reactions. Journal of Chemical Physics 89(2):859, doi:10.1063/1.455719.
105. S. Creighton, J. K. Hwang, A. Warshel, W. W. Parson, & J. Norris (1988) Simulating the Dynamics of the Primary Charge Separation Process in Bacterial Photosynthesis. Biochemistry 27(2):774, doi:10.1021/bi00402a043.
104. A. Warshel & W. W. Parson (1987) Spectroscopic Properties of Photosynthetic Reaction Centers .1. Theory. Journal of the American Chemical Society 109(20):6143, doi:10.1021/ja00254a039.
103. A. Warshel (1987) Activation Free Energies of Enzymatic Reactions Simulations and Experiments. Ehrenberg, A., Et Al., Springer Series in Biophysics), pp 61.
99. A. Warshel (1987) Evaluating Catalytic Free-Energy in Enzymes. Biochemistry 26(13):4158.
98. A. Warshel (1987) Molecular Biophysics - What About Protein Polarity. Nature 330(6143):15, doi:10.1038/330015a0.
96. W. W. Parson & A. Warshel (1987) Spectroscopic Properties of Photosynthetic Reaction Centers .2. Application of the Theory to Rhodopseudomonas-Viridis. Journal of the American Chemical Society 109(20):6152, doi:10.1021/ja00254a040.
95. J. K. Hwang & A. Warshel (1987) Microscopic Examination of Free-Energy Relationships for Electron-Transfer in Polar-Solvents. Journal of the American Chemical Society 109(3):715, doi:10.1021/ja00237a013.
94. J. K. Hwang & A. Warshel (1987) Semiquantitative Calculations of Catalytic Free-Energies in Genetically Modified Enzymes. Biochemistry 26(10):2669, doi:10.1021/bi00384a003.
93. A. Warshel, F. Sussman, & G. King (1986) Free-Energy of Charges in Solvated Proteins - Microscopic Calculations Using a Reversible Charging Process. Biochemistry 25(26):8368, doi:10.1021/bi00374a006.
91. A. Warshel & F. Sussman (1986) Toward Computer-Aided Site-Directed Mutagenesis of Enzymes. Proceedings of the National Academy of Sciences of the United States of America 83(11):3806, doi:10.1073/pnas.83.11.3806.
90. A. Warshel, S. Russell, & F. Sussman (1986) Computer-Simulation of Enzymatic-Reactions. Israel Journal of Chemistry 27(2):217.
89. A. Warshel & S. Russell (1986) Theoretical Correlation of Structure and Energetics in the Catalytic Reaction of Trypsin. Journal of the American Chemical Society 108(21):6569, doi:10.1021/ja00281a021.
88. A. Warshel & J. K. Hwang (1986) Simulation of the Dynamics of Electron-Transfer Reactions in Polar-Solvents - Semiclassical Trajectories and Dispersed Polaron Approaches. Journal of Chemical Physics 84(9):4938, doi:10.1063/1.449981.
87. A. Warshel (1986) Correlation between the Structure and Efficiency of Light-Induced Proton Pumps. Methods in Enzymology 127:578.
83. A. K. Churg & A. Warshel (1986) Control of the Redox Potential of Cytochrome-C and Microscopic Dielectric Effects in Proteins. Biochemistry 25(7):1675, doi:10.1021/bi00355a035.
81. A. Warshel & G. King (1985) Polarization Constraints in Molecular-Dynamics Simulation of Aqueous-Solutions - the Surface Constraint All Atom Solvent (Scaas) Model. Chemical Physics Letters 121(1-2):124, doi:10.1016/0009-2614(85)87168-2.
80. A. Warshel & J. K. Hwang (1985) Quantized Semiclassical Trajectory Approach for Evaluation of Vibronic Transitions in Anharmonic Molecules. Journal of Chemical Physics 82(4):1756, doi:10.1063/1.448408.
79. S. T. Russell & A. Warshel (1985) Calculations of Electrostatic Energies in Proteins - the Energetics of Ionized Groups in Bovine Pancreatic Trypsin-Inhibitor. Journal of Molecular Biology 185(2):389, doi:10.1016/0022-2836(85)90411-5.
78. J. K. Hwang & A. Warshel (1985) Semiclassical Simulations of the Spectra of Anharmonic Molecules - Problems and Alternatives. Chemical Physics Letters 115(3):281, doi:10.1016/0009-2614(85)80028-2.
77. J. K. Hwang & A. Warshel (1985) A Shortcut for Multidimensional Quantization - the Average Partial Actions Method. Chemical Physics Letters 118(3):289, doi:10.1016/0009-2614(85)85318-5.
76. A. K. Churg & A. Warshel (1985) Modeling the Activation Energy and Dynamics of Electron Transfer Reactions in Proteins pp 361.
76. Warshel, A. (1984). Simulating the Energetics and Dynamics of Enzymatic Reactions. In: Chagas, C., Pullman, B. (eds) Specificity in Biological Interactions. Springer, Dordrecht. doi.org/10.1007/978-94-009-6457-0_4
75. A. Warshel, S. T. Russell, & A. K. Churg (1984) Macroscopic Models for Studies of Electrostatic Interactions in Proteins - Limitations and Applicability. Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences 81(15):4785, doi:10.1073/pnas.81.15.4785.
74. A. Warshel & S. T. Russell (1984) Calculations of Electrostatic Interactions in Biological-Systems and in Solutions. Quarterly Reviews of Biophysics 17(3):283.
73. A. Warshel (1984) Dynamics of Enzymatic-Reactions. Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences 81(2):444, doi:10.1073/pnas.81.2.444.
72. A. Warshel, P. S. Stern, & S. Mukamel (1983) Semiclassical Calculation of Electronic-Spectra of Supercooled Anharmonic Molecules. Journal of Chemical Physics 78(12):7498, doi:10.1063/1.444708.
71. A. Warshel & A. K. Churg (1983) Converting Structural-Changes Upon Oxidation of Cytochrome-C to Electrostatic Reorganization Energy. Journal of Molecular Biology 168(3):693, doi:10.1016/s0022-2836(83)80310-6.
68. A. K. Churg, R. M. Weiss, A. Warshel, & T. Takano (1983) On the Action of Cytochrome-C - Correlating Geometry Changes Upon Oxidation with Activation-Energies of Electron-Transfer. Journal of Physical Chemistry 87(10):1683, doi:10.1021/j100233a010.
67. A. Warshel & N. Barboy (1982) Energy-Storage and Reaction Pathways in the 1st Step of the Vision Process. Journal of the American Chemical Society 104(6):1469, doi:10.1021/ja00370a003.
66. A. Warshel (1982) Dynamics of Reactions in Polar-Solvents - Semi-Classical Trajectory Studies of Electron-Transfer and Proton-Transfer Reactions. Journal of Physical Chemistry 86(12):2218, doi:10.1021/j100209a016.
64. A. Warshel & R. M. Weiss (1981) Energetics of Heme-Protein Interactions in Hemoglobin. Journal of the American Chemical Society 103(2):446, doi:10.1021/ja00392a033.
63. A. Warshel & D. W. Schlosser (1981) Electrostatic Control of the Efficiency of Light-Induced Electron-Transfer across Membranes. Proceedings of the National Academy of Sciences of the United States of America-Biological Sciences 78(9):5564, doi:10.1073/pnas.78.9.5564.
62. A. Warshel & A. Lappicirella (1981) Calculations of Ground-Excited and Excited-State Potential Surfaces for Conjugated Heteroatomic Molecules. Journal of the American Chemical Society 103(16):4664, doi:10.1021/ja00406a002.
61. A. Warshel (1981) Energetics of Light-Induced Charge Separation across Membranes. Israel Journal of Chemistry 21(4):341.
60. A. Warshel (1981) Calculations of Enzymatic-Reactions - Calculations of Pka, Proton-Transfer Reactions, and General Acid Catalysis Reactions in Enzymes. Biochemistry 20(11):3167, doi:10.1021/bi00514a028.
59. A. Warshel (1981) Electrostatic Basis of Structure-Function Correlation in Proteins. Accounts of Chemical Research 14(9):284, doi:10.1021/ar00069a004.
58. A. Warshel & R. M. Weiss (1980) An Empirical Valence Bond Approach for Comparing Reactions in Solutions and in Enzymes. Journal of the American Chemical Society 102(20):6218, doi:10.1021/ja00540a008.
57. A. Warshel (1980) Role of the Chlorophyll Dimer in Bacterial Photosynthesis. Proceedings of the National Academy of Sciences of the United States of America-Physical Sciences 77(6):3105, doi:10.1073/pnas.77.6.3105.
56. R. M. Weiss & A. Warshel (1979) New View of the Dynamics of Singlet Cis-Trans Photoisomerization. Journal of the American Chemical Society 101(20):6131, doi:10.1021/ja00514a051.
55. A. Warshel & M. Ottolenghi (1979) Kinetic and Spectroscopic Effects of Protein-Chromophore Electrostatic Interactions in Bacteriorhodopsin. Photochemistry and Photobiology 30(2):291, doi:10.1111/j.1751-1097.1979.tb07149.x.
54. A. Warshel (1979) Conversion of Light Energy to Electrostatic Energy in the Proton Pump of Halobacterium-Halobium. Photochemistry and Photobiology 30(2):285, doi:10.1111/j.1751-1097.1979.tb07148.x.
53. A. Warshel (1979) Origin of the Red Shift of the Absorption-Spectra of Aggregated Chlorophylls. Journal of the American Chemical Society 101(3):744, doi:10.1021/ja00497a047.
52. A. Warshel (1979) Calculations of Chemical Processes in Solutions. Journal of Physical Chemistry 83(12):1640, doi:10.1021/j100475a014.
51. A. Warshel & C. Deakyne (1978) Coupling of Charge Stabilization, Torsion and Bond Alternation in Light-Induced Reactions of Visual Pigments. Chemical Physics Letters 55(3):459, doi:10.1016/0009-2614(78)84014-7.
50. A. Warshel (1978) Energetics of Enzyme Catalysis. Proceedings of the National Academy of Sciences of the United States of America 75(11):5250, doi:10.1073/pnas.75.11.5250.
49. A. Warshel (1978) Charge Stabilization Mechanism in Visual and Purple Membrane Pigments. Proceedings of the National Academy of Sciences of the United States of America 75(6):2558, doi:10.1073/pnas.75.6.2558.
48. A. Warshel (1978) Microscopic Model for Calculations of Chemical Processes in Aqueous-Solutions. Chemical Physics Letters 55(3):454, doi:10.1016/0009-2614(78)84013-5.
47. A. Warshel (1978) General Anharmonicity Treatments for Large Molecules and Local Modes Description. Bulletin of the American Physical Society 23(1):78.
46. R. Liang, O. Schnepp, & A. Warshel (1978) Resonance Raman-Spectrum of Azulene. Chemical Physics 34(1):17, doi:10.1016/0301-0104(78)87101-8.
45. M. Levitt & A. Warshel (1978) Extreme Conformational Flexibility of Furanose Ring in DNA and Rna. Journal of the American Chemical Society 100(9):2607, doi:10.1021/ja00477a004.
44. M. D. Cohen, R. Haberkorn, E. Huler, Z. Ludmer, M. E. Michelbeyerle, D. Rabinovich, R. Sharon, A. Warshel, & V. Yakhot (1978) Pair-States in Alpha-Perylene Crystal - Theoretical-Study. Chemical Physics 27(2):211, doi:10.1016/0301-0104(78)88005-7.
43. A. Warshel & P. Dauber (1977) Calculations of Resonance Raman-Spectra of Conjugated Molecules. Journal of Chemical Physics 66(12):5477, doi:10.1063/1.433867.
42. A. Warshel (1977) Interpretation of Resonance Raman Spectra of Biological Molecules pp 273.
41. A. Warshel (1977) How Do Enzymes Really Work pp 574.
40. A. Warshel (1977) Energy-Structure Correlation in Metalloporphyrins and Control of Oxygen Binding by Hemoglobin. Proceedings of the National Academy of Sciences of the United States of America 74(5):1789, doi:10.1073/pnas.74.5.1789.
39. A. Warshel (1977) Qcff-Pi+Mca Program Package Efficiency and Versatility in Molecular Mechanics. Computers & Chemistry 1(3):195, doi:10.1016/0097-8485(77)85010-9.
38. A. Warshel (1977) Interpretation of Resonance Raman-Spectra of Biological Molecules. Annual Review of Biophysics and Bioengineering 6:273, doi:10.1146/annurev.bb.06.060177.001421.
37. F. H. Stillinger, J. B. Hasted, & A. Warshel (1977) Theoretical Approaches to Intermolecular Nature of Water. Philosophical Transactions of the Royal Society of London Series B-Biological Sciences 278(959):97, doi:10.1098/rstb.1977.0033.
36. A. Warshel & M. Levitt (1976) Theoretical Studies of Enzymic Reactions - Dielectric, Electrostatic and Steric Stabilization of Carbonium-Ion in Reaction of Lysozyme. Journal of Molecular Biology 103(2):227, doi:10.1016/0022-2836(76)90311-9.
35. A. Warshel & M. Levitt (1976) Folding and Stability of Helical Proteins - Carp Myogen. Journal of Molecular Biology 106(2):421, doi:10.1016/0022-2836(76)90094-2.
34. A. Warshel (1976) Orbitals, Conformation and Biological-Activity - Theoretical Studies of Drug Receptor Interaction. Trends in Biochemical Sciences 1(5):N105, doi:10.1016/0968-0004(76)90308-x.
33. A. Warshel (1976) Bicycle-Pedal Model for 1st Step in Vision Process. Nature 260(5553):679, doi:10.1038/260679a0.
32. A. Warshel (1976) Molecular Origin of Anomalous Polarization in Resonance Raman of Metalloporphyrins. Chemical Physics Letters 43(2):273, doi:10.1016/0009-2614(76)85301-8.
30. R. Liang, O. Schnepp, & A. Warshel (1976) Resonance Raman-Spectrum of Azulene. Chemical Physics Letters 44(2):394, doi:10.1016/0009-2614(76)80537-4.
29. A. Warshel & Z. Shakked (1975) Theoretical-Study of Excimers in Crystals of Flexible Conjugated Molecules - Excimer Formation and Photodimerization in Crystalline 1,4-Diphenylbutadiene. Journal of the American Chemical Society 97(20):5679, doi:10.1021/ja00853a006.
28. A. Warshel & M. Karplus (1975) Semiclassical Trajectory Approach to Photoisomerization. Chemical Physics Letters 32(1):11, doi:10.1016/0009-2614(75)85157-8.
26. A. Warshel (1975) Calculation of Vibronic Structure of Pi- Pi Transition of Trans-Stilbene and Cis-Stilbene. Journal of Chemical Physics 62(1):214, doi:10.1063/1.430265.
25. M. Levitt & A. Warshel (1975) Computer-Simulation of Protein Folding. Nature 253(5494):694, doi:10.1038/253694a0.
24. E. Huler & A. Warshel (1975) Consistent Calculation of Lattice-Dynamics Using Semiempirical Potential Functions. Chemical Physics 8(1-2):239, doi:10.1016/0301-0104(75)80113-3.
23. B. Honig, A. Warshel, & M. Karplus (1975) Theoretical Studies of Visual Chromophore. Accounts of Chemical Research 8(3):92, doi:10.1021/ar50087a003.
22. P. Dauber, M. Brith, E. Huler, & A. Warshel (1975) Vibronic Structure of Crystalline Ethylene. Chemical Physics 7(1):108, doi:10.1016/0301-0104(75)85030-0.
21. A. Warshel & M. Karplus (1974) Calculation of Pi Pi Excited-State Conformations and Vibronic Structure of Retinal and Related Molecules. Journal of the American Chemical Society 96(18):5677,doi:10.1021/ja00825a001.
20. A. Warshel, E. Huler, Rabinovi.D, & Z. Shakked (1974) Examination of Intramolecular Potential Surfaces of Flexible Conjugated Molecules by Calculation of Crystal-Structures - Equilibrium Geometries of Chalcones and Diphenyloctatetraene in Crystal and Gaseous State. Journal of Molecular Structure 23(2):175, doi:10.1016/0022-2860(74)85032-5.
19. A. Warshel & E. Huler (1974) Theoretical Evaluation of Potential Surfaces, Equilibrium Geometries and Vibronic Transition Intensities of Excimers - Pyrene Crystal Excimer. Chemical Physics 6(3):463, doi:10.1016/0301-0104(74)85030-5.
18. Schlessi.J & A. Warshel (1974) Calculations of Cd and Cpl Spectra as a Tool for Evaluation of Conformational Differences between Ground and Excited-States of Chiral Molecules. Chemical Physics Letters 28(3):380, doi:10.1016/0009-2614(74)80370-2.
17. R. Rowan, A. Warshel, B. D. Sykes, & M. Karplus (1974) Conformation of Retinal Isomers. Biochemistry 13(5):970, doi:10.1021/bi00702a022.
16. E. Huler & A. Warshel (1974) Incorporation of Intermolecular and Intramolecular Forces in Calculation of Crystal Packing and Lattice-Vibrations. Acta Crystallographica Section B-Structural Science B 30(JUL15):1822, doi:10.1107/s0567740874005875.
15. B. Hudson, A. Warshel, & R. G. Gordon (1974) Molecular Inelastic Neutron-Scattering - Computational Methods Using Consistent Force-Fields. Journal of Chemical Physics 61(7):2929, doi:10.1063/1.1682435.
14. A. Warshel (1973) Quantum-Mechanical Consistent Force-Field (Qcff/Pi) Method - Calculations of Energies, Conformations and Vibronic Interactions of Ground and Excited-States of Conjugated Molecules. Israel Journal of Chemistry 11(5):709.
13. A. Warshel & M. Karplus (1972) Calculation of Ground and Excited-State Potential Surfaces of Conjugated Molecules .1. Formulation and Parametrization. Journal of the American Chemical Society 94(16):5612, doi:10.1021/ja00771a014.
12. A. Warshel & M. Karplus (1972) Vibrational Structure of Electronic Transitions in Conjugated Molecules. Chemical Physics Letters 17(1):7, doi:10.1016/0009-2614(72)80311-7.
11. A. Warshel (1971) Anharmonicity in Crystal Vibrations. Journal of Chemical Physics 54(12):5324, doi:10.1063/1.1674831.
10. A. Warshel (1971) Calculation of Anharmonicity in Vibrational Frequencies of Alkane Molecules by Cff Functions. Journal of Chemical Physics 55(7):3327, doi:10.1063/1.1676584.
9. A. Warshel & S. Lifson (1970) Consistent Force Field Calculations .2. Crystal Structures, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations, and Enthalpies of Alkanes. Journal of Chemical Physics 53(2):582, doi:10.1063/1.1674031.
8. A. Warshel, M. Levitt, & S. Lifson (1970) Consistent Force Field for Calculation of Vibrational Spectra and Conformations of Some Amides and Lactam Rings. Journal of Molecular Spectroscopy 33(1):84, doi:10.1016/0022-2852(70)90054-8.
7. A. Warshel & A. Bromberg (1970) Oxidation of 4a,4b-Dihydrophenanthrenes .3. A Theoretical Study of Large Kinetic Isotope Effect of Deuterium in Initiation Step of Thermal Reaction with Oxygen. Journal of Chemical Physics 52(3):1262, doi:10.1063/1.1673124.
6. T. S. Kuan, A. Warshel, & O. Schnepp (1970) Intermolecular Potentials for N2 Molecules and Lattice Vibrations of Solid Alpha-N2. Journal of Chemical Physics 52(6):3012, doi:10.1063/1.1673432.
5. A. Bromberg, K. A. Muszkat, & A. Warshel (1970) Oxidation of 4a,4b-Dihydrophenanthrene .4. Kinetic Isotope Effect of Deuterium in Propagation and Initiation Steps. Journal of Chemical Physics 52(11):5952, doi:10.1063/1.1672879.
4. A. Warshel & S. Lifson (1969) Toward a Better Description of Potential Surface of Alkanes. Israel Journal of Chemistry 7:P59.
3. A. Warshel & S. Lifson (1969) An Empirical Function for Second Neighbor Interactions and Its Effect on Vibrational Modes and Other Properties of Cyclo- and N-Alkanes. Chemical Physics Letters 4(5):255, doi:10.1016/0009-2614(69)80177-6.
2. T. S. Kuan, A. Warshel, & O. Schnepp (1969) Intemolecular Potentials for N2 Molecules and Lattice Vibrations of Solid Alpha-N2. Bulletin of the American Physical Society 14(12):1186.
1. S. Lifson & A. Warshel (1968) Consistent Force Field for Calculations of Conformations Vibrational Spectra and Enthalpies of Cycloalkane and N-Alkane Molecules. Journal of Chemical Physics 49(11):5116, doi:10.1063/1.1670007.
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