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Objective
We study computational biology and simulations to decipher the elemental processes and to help alleviate human suffering. The methods developed in our lab allow for the prediction of how chemical reactions in enzymes and solutions can lead to more efficient chemical processes and the development of new and effective drugs."
"As one of the pioneers of using computer simulations for complex molecular systems, I learned since the late 60s to use very limited resources to capture the main physics of biological systems, without consuming enormous computer power." Arieh Warshel.
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Method
Professor Warshel and his research team leverage their knowledge of chemistry, biology and computer science to simulate biological systems to better understand their structure and function. This methodology has pioneered highly effective models for computer simulations of biological molecules, chemical reactions, and interactive drug therapies.
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Evaluation
The Warshel research group operates 38 dedicated compute nodes on The University of Southern California HPC, all based on Intel CPU architecture and capable of achieving a benchmark of 12.2 trillion floating-point calculations per second. Our lab operates 5 home-based dedicated compute servers (also based on Intel CPU architecture) that can add another 5.18 trillion floating-point calculations per second to the total compute capacity available to group's members.
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Critical Differences Between the Binding Features of the Spike Proteins of SARS-CoV-2 and SARS-CoV.
Chen Bai and Arieh Warshel
The Journal of Physical Chemistry B, 2020, June 17, 2020
doi: 10.1021/acs.jpcb.0c04317
Exploring the Proteolysis Mechanism of the Proteasomes
Arjun Saha, Gabriel Oanca, Dibyendu Mondal, and Arieh Warshel
The Journal of Physical Chemistry B, 2020, June 4, 2020;XXXX, XXX, XXX-XXX
doi: 10.1021/acs.jpcb.0c04435
Combinatorial Approach for Exploring Conformational Space and Activation Barriers in Computer-Aided Enzyme Design.
Dibyendu Mondal, Vesselin Kolev, and Arieh Warshel
ACS Catalysis, 2020, 10, 11:6002-6012
doi: 10.1021/acscatal.0c01206
Exploring alternative catalytic mechanisms of the Cas9 HNH domain.
Zhao LN, Mondal D, Warshel A
Proteins, 2020, Feb;88(2):260-264
doi: 10.1002/prot.25796
A free-energy landscape for the glucagon-like peptide 1 receptor GLP1R.
Alhadeff R, Warshel A,
Proteins, 2020, Jan;88(1):127-134
doi: 10.1002/prot.25777
Exploring the Effectiveness of Binding Free Energy Calculations.
Mondal D, Florian J, Warshel A,
J Phys Chem B, 2019, Oct 24;123(42):8910-8915
doi: 10.1021/acs.jpcb.9b07593
Revisiting the protomotive vectorial motion of F0-ATPase.
Bai C, Warshel A,
Proc Natl Acad Sci USA, 2019, Sep 24;116(39):19484-19489
doi: 10.1073/pnas.1909032116
ZnT2 is an electroneutral proton-coupled vesicular antiporter displaying an apparent stoichiometry of two protons per zinc ion.
Golan Y, Alhadeff R, Warshel A, Assaraf YG
PLoS Comput Biol. 2019, Mar;15(3):e1006882
doi: 10.1371/journal.pcbi.1006882
Exploring the challenges of computational enzyme design by rebuilding the active site of a dehalogenase.
Jindal G, Slanska K, Kolev V, Damborsky J, Prokop Z, Warshel A
Proc Natl Acad Sci U S A, 2019, Jan 8;116(2):389-394
doi: 10.1073/pnas.1804979115
Demonstrating aspects of multiscale modeling by studying the permeation pathway of the human ZnT2 zinc transporter
Golan Y, Alhadeff R, Glaser F, Ganoth A, Warshel A, Assaraf YG
PLoS Comput Biol, 2018, Nov;14(11):e1006503
doi: 10.1371/journal.pcbi.1006503