Publications : Methods

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Application of new informatics tools for identifying allosteric lead ligands of the c-Src kinase

BioRxiv: 038323, 2016
Peng, Lili X and Lawrenz, Morgan and Shukla, Diwakar and Tang, Grace W and Pande, Vijay S and Altman, Russ B
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Transition path theory analysis of c-Src kinase activation

Proceedings of the National Academy of Sciences, 113(33): 9193-9198, 2016
Yilin Meng and Diwakar Shukla and Vijay S. Pande and Beno^it Roux
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Elucidating ligand-modulated conformational landscape of GPCRs using cloud-computing approaches

Methods in Enzymology, Elsevier, 557: 551-572, 2015
Shukla, Diwakar and Lawrenz, Morgan and Pande, Vijay S
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Heat dissipation guides activation in signaling proteins

Proceedings of the National Academy of Sciences, 112(33): 10377-10382, 2015
Jeffrey K. Weber and Diwakar Shukla and Vijay S. Pande
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Markov State Models Provide Insights into Dynamic Modulation of Protein Function

Accounts of Chemical Research, 48(2): 414-422, 2015
Diwakar Shukla and Carlos X. Hern’andez and Jeffrey K. Weber and Vijay S. Pande
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Cloud computing approaches for prediction of ligand binding poses and pathways

Scientific Reports, 5(1), 2015
Morgan Lawrenz and Diwakar Shukla and Vijay S. Pande
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Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics

Journal of Chemical Theory and Computation, 11(3): 1094-1101, 2015
Matthew P. Harrigan and Diwakar Shukla and Vijay S. Pande
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Automatic Selection of Order Parameters in the Analysis of Large Scale Molecular Dynamics Simulations

Journal of Chemical Theory and Computation, 10(12): 5217-5223, 2014
Mohammad M. Sultan and Gert Kiss and Diwakar Shukla and Vijay S. Pande
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Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways

Nature Chemistry, 6(1): 15-21, 2013
Kai J. Kohlhoff and Diwakar Shukla and Morgan Lawrenz and Gregory R. Bowman and David E. Konerding and Dan Belov and Russ B. Altman and Vijay S. Pande
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OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

Journal of Chemical Theory and Computation, 9(1): 461-469, 2012
Peter Eastman and Mark S. Friedrichs and John D. Chodera and Randall J. Radmer and Christopher M. Bruns and Joy P. Ku and Kyle A. Beauchamp and Thomas J. Lane and Lee-Ping Wang and Diwakar Shukla and Tony Tye and Mike Houston and Timo Stich and Christoph Klein and Michael R. Shirts and Vijay S. Pande
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