Arieh warshel



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-3340 (2012).




  1. Towards Quantitative Computer-Aided Studies of Enzymatic Enantioselectivity: The Case of Candida antarctica Lipase A, M. Frushicheva and A. Warshel, ChemBiochem 13, 215-223 (2012).




  1. Validating the Vitality Strategy for Fighting Drug Resistance, N. Singh, M. P. Frushicheva and A. Warshel, Proteins 80, 1110-1122 (2012).




  1. Realistic Simulations of the Coupling Between the Protomotive Force and the Mechanical Rotation of the F0-ATPase, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 109, 14876-14881 (2012).




  1. Exploring, Refining, and Validating the Paradynamics QM/MM Sampling, N.V. Plotnikov and A. Warshel, J. Phys. Chem. B 116, 10342-10356 (2012).




  1. Origin of Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in SN2 Reactions, E. Rosta and A. Warshel. J. Chem. Theory Comput. 8, 3574-3585 (2012).




  1. Catalytic Effects of Mutations of Distant Protein Residues in Human DNA Polymerase β: Theory and Experiment, M. Klvaňa, D. L. Murphy, P. Jerǎb́ek, M.F. Goodman, A. Warshel, B. Sweasy, and J. Floriań, Biochemistry 51, 8829-8843 (2012).

  2. Electrostatic Origin of the Catalytic Effect of a Supramolecular Host Catalyst, M. P. Frushicheva, S. Mukherjee and A. Warshel, J. Phys. Chem. B 116, 13353-13360 (2012).

  3. Prechemistry Barriers and Checkpoints Do Not Contribute to Fidelity and Catalysis, as Long as They Are Not Rate Limiting, B. R. Prasad, S. C. L. Kamerlin, J. Floria´n and A. Warshel, Theor. Chem. Acc. 131, 1288-1302 (2012).




  1. Studying Catalysis by QM/MM Approaches Should Not be a Black Box Process B. R. Prasad, S. C. L. Kamerlin, N. V. Plotnikov and A. Warshel, J. Thermodyn. Catal. 3, 2-4 (2012).




  1. Capturing the Energetics of Water Insertion in Biological Systems: The Water Flooding Approach, S. Chakrabarty and A. Warshel, Proteins 81, 93-106 (2013).




  1. Why Nature Really Chose Phosphate, S.C.L. Kamerlin., P.B. Sharma, R.B. Prasad and A. Warshel, Q. Rev. Biophys. 46, 1-132 (2013).




  1. Addressing Open Questions about Phosphate Hydrolysis Pathways by Careful Free Energy Mapping, B. R. Prasad, N. V. Plotnikov, and A. Warshel, J. Phys. Chem. B 117, 153-163 (2013).




  1. Exploring the Nature of the Translocon-Assisted Protein Insertion, A. Rychkova and A. Warshel, Proc. Natl. Acad. Sci. USA 110, 495-500 (2013).




  1. Quantifying the Mechanism of Phosphate Monoester Hydrolysis in Aqueous Solution by Evaluating the Relevant Ab Initio QM/MM Free Energy Surfaces, N. V. Plotnikov, R. B. Prasad, S. Chakrabarty, Z. T. Chu and A. Warshel, J. Phys. Chem. B 117, 12807-12819 (2013).




  1. Simulating the Pulling of Stalled Elongated Peptide from the Ribosome by the Translocon, A. Rychkova, S. Mukherjee, R. P. Bora, and A. Warshel, Proc. Natl. Acad. Sci. USA 110, 10195-10200 (2013).




  1. How do Enzymes Really Work? The Dawn of Simulating Biological Functions (1974-5) in “Memories and Consequences: Visiting scientists at the MRC Laboratory of Molecular Biology, Cambridge, Published by the MRC, ed. Hugh Huxley, 271-281, (2013).




  1. Electrostatic Origin of the Unidirectionality of Walking Myosin V Motors, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 110, 17326-17331 (2013).




  1. Quantitative Exploration of the Molecular Origin of the Activation of GTPase, R. B. Prasad, N. V. Plotnikov, J. Lameira and A. Warshel, Proc. Natl. Acad. Sci. USA 110, 20509-20514 (2013).




  1. On the Nature of the Apparent Free Energy of Inserting Amino Acids into Membrane through the Translocon, A. Rychkova and A. Warshel, J. Phys. Chem. B 117, 13748-13754 (2013).




  1. Coarse-Grained Simulation of the Gating Current in the Voltage-Activation Kv1.2 Channel, I. Kim and A. Warshel, Proc. Natl. Acad. Sci. USA 111, 2128-2133 (2013).




  1. Response to Vilfan: Constructing Structure-Based Free Energy Surfaces is the Key to Understand Myosin V Unidirectionality, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 111, 2077 (2014).




  1. An Effective Coarse-Grained Model for Biological Simulations: Recent Refinements and Validations, S. Vicatos, A. Rychkova, S. Mukherjee and A. Warshel, Proteins 82, 1168-1185 (2014).




  1. Validating Computer Simulations of Enantioselective Catalysis; Reproducing the Large Steric and Entropic Contributions in Candida Antarctica Lipase B, P. Schopf and A. Warshel, Proteins 82, 1387-1399 (2014).




  1. Modeling Gating Charge and Voltage Changes in Response to Charge Separation in Membrane Proteins, I. Kim, S. Chakrabarty, P. Brzezinski, and A. Warshel, Proc. Natl. Acad. Sci. USA 111, 11353-11358 (2014).




  1. Computer Aided Enzyme Design and Catalytic Concepts, M.P. Frushicheva, M.J.L. Mills, P. Schopf, M.K. Singh, R.B. Prasad, and A. Warshel, Curr. Opin. Chem. Biol. 21, 56-62 (2014).




  1. Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture), A. Warshel, Angew. Chem. Int. Ed., 53, 10020-10031 (2014).




  1. Simulating the Catalytic Effect of a Designed Mononuclear Zinc Metalloenzyme that Catalyzes the Hydrolysis of Phosphate Triesters, M.K. Singh, Z.T. Chu, and A. Warshel, J. Phys. Chem. B, 118, 12146-12152 (2014).




  1. Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization, Lameira J, B RP, Chu ZT, Warshel A, Proteins 83, 318-330 (2014).




  1. Dissecting the role of the γ-subunit in the rotary– chemical coupling and torque generation of F1-ATPase, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 112, 2746-2751 (2015).




  1. The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm, P. Schopf, M. J. L. Mills and A. Warshel, Proc. Natl. Acad. Sci. USA,112, 4328-4333 (2015).




  1. On the Challenge in Exploring the Evolutionary Trajectory from Phosphotriesterase to Arylesterase Using Computer Simulations, R. B. Prasad, M. J. L. Mills, M. P. Frushicheva, and A. Warshel, J. Phys. Chem. B, 119, 3434-3445, (2015).




  1. Torque, chemistry and efficiency in molecular motors: a study of the rotary–chemical coupling in F1-ATPase, S. Mukherjee, R. B. Prasad and A. Warshel, QRB, Discovery, 48, 395–403 (2015).




  1. Simulating the function of sodium/proton antiporters, R. Alhadeff and A. Warshel, Proc. Natl. Acad. Sci. USA,112, 12378–12383 (2015).




  1. Brønsted slopes based on single-molecule imaging data help to unveil the chemically coupled rotation in F1-ATPase, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 112,14121–14122 (2015).




  1. Equilibrium fluctuation relations for voltage coupling in membrane proteins, I. Kim, and A. Warshel, Biochimica et Biophysica Acta, 1848, 2985–2997 (2015).




  1. Refining the treatment of membrane proteins by coarse-grained models, I. Vorobyov, I. Kim, Z. T. Chu, and A. Warshel, PROTEINS, 84, 92–117 (2016).




  1. A Microscopic Capacitor Model of Voltage Coupling in Membrane Proteins: Gating Charge Fluctuations in Ci-VSD, I. Kim and A. Warshel, JPC B, 120, 418-32 (2016).




  1. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis, Arieh Warshel and R. B. Prasad, J. Chem. Phys.144, 180901-17 (2016).




  1. The Physics and Physical Chemistry of Molecular Machines, R.D. Astumian,S. Mukherjee and A. Warshel, Chemphyschem 17, 1719-1741 (2016).




  1. Exploring the dependence of QM/MM calculations of enzyme catalysis on the size of the QM region. G. Jindal G and A. Warshel, J Phys Chem B 120: 9913-21 (2016).




  1. Simulating the function of the MjNhaP1 transporter, R. Alhadeff and A. Warshel J. Phys. Chem. B, 120, 10951-58 (2016).




  1. Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions, J. Lameira ,I. Kupchencko and A. Warshel, J. Phys. Chem B, 120, 2155-64 (2016).




  1. The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase, H. Yoon and A. Warshel, Proteins, 84, 1616-24 (2016).




  1. Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β, R. A. Matute, H. Yoon, and Arieh Warshel, Proteins, 84, 1644-57 (2016).




  1. A personal perspective on calculations of binding free energies, H. Yoon and A. Warshel, Chemistry, Molecular Sciences and Chemical Engineering, online (2016).




  1. Perspective on computer modeling of enzymatic reactions, A. Warshel and R. P. Bora., In: Inaki Tunon, Vicent Moliner, editors. Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis, Cambridge: RSC, 1-30 (2017).




  1. Simulating the Dynamics of The Mechanochemical Cycle of Myosin-V, S. Mukherjee, R. Alhadeff, and A. Warshel, Proc. Natl. Acad. Sci. USA, 114, 2259-64 (2017).




  1. Exploring the Design of Kemp Eliminase and the nature of two directed evolution paths, G. Jindal, B. Ramachandran, R. Prasad and A. Warshel, ACS Catalysis, 7, 3301-05 (2017).




  1. On the origin of non-Arrhenius behavior of the rates of enzymatic reactions, S. Roy, P. Schopf and A, Warshel, JPC B, 121, 6520-26 (2017).




  1. Exploring the drug resistance of HCV Protease, G. Jindal, D. Mondal and A. Warshel, JPC B, 121, 6831-40 (2017).




  1. Simulating the Fidelity and The Three Mg Mechanism of Pol  and clarifying the validity of transition state theory in enzyme catalysis, Hanwool Yoon and A. Warshel, Proteins, 85, 1446-53(2017).


BOOKS


1991 Computer Simulation of Chemical Reactions in Enzymes and Solutions, A. Warshel, John Wiley &Sons, (1991).
1997 Computational Approaches to Biochemical Reactivity, G. Naray-Szabo and A. Warshel, eds., Kluwer, Academic Publishers, (1997).


COMPUTER PROGRAMS


QCFF/PI: A Program for the Consistent Force Field Evaluation of Equilibrium Geometries and Vibrational Frequencies of Molecules, A. Warshel and M. Levitt, QCPE 247, Quantum Chemistry Program Exchange, Indiana University (1974).
MCA: Molecular Crystals Analysis, E. Huler and A. Warshel, QCPE 325, Quantum Chemistry Program Exchange, Indiana University (1976).
MOLARIS: A General Program Package for Simulations of Macromolecules (1989).
POLARIS: A Program for PDLD Calculations of Electrostatic Energies in Solution and Proteins (1989).
ENZYMIX: A General for Simulations of Chemical Processes in Enzymes and Solutions (1989).

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