Publications : Methods

Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity

The Journal of Physical Chemistry B, 121(42): 9761-9770, 2017
Shriyaa Mittal and Diwakar Shukla
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Application of hidden Markov models in biomolecular simulations

Hidden Markov Models, Springer: 29-41, 2017
Shukla, Saurabh and Shamsi, Zahra and Moffett, Alexander S and Selvam, Balaji and Shukla, Diwakar
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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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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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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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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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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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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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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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