Publications - Stanford

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Markov State Model Reveals Slow Folding Phase of NuG2.

Stanford
C. Schwantes, D. Shukla & V. S. Pande,
Biophysical Journal, Volume 110, Issue 8, p1716–1719, 2016.

A Transition Path Theory Analysis of The Activating Transition in c-Src Kinase Domain

Faculty of 1000 (F1000)Stanford
Yilin Meng, Diwakar Shukla, Vijay Pande and Benoît Roux
Proceedings of the National Academy of Sciences, Vol. 113, No. 33, 9193–9198, 2016.

Conformational Heterogeneity of the Calmodulin Binding Interface.

IllinoisStanford
Diwakar Shukla*, Ariana Peck* and Vijay S. Pande
Nature Communications, 7, Article number: 10910, 2016. doi:10.1038/ncomms10910

Heat Dissipation Guides Activation in Signaling Proteins

Stanford
Jeffrey K. Weber, Diwakar Shukla, and Vijay S. Pande
Proceedings of National Academy of Sciences USA, 112, 33, 10377–10382, 2015.

A Network of Molecular Switches Control the Activation of Key Bacterial Signaling Protein

Stanford
Dan K. Vanatta, Diwakar Shukla, Morgan Lawrenz & Vijay S. Pande
Nature Communications, 6, Article number: 7283, 2015. doi:10.1038/ncomms8283

Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-computing Approaches.

Book ChapterIllinoisStanford
Diwakar Shukla*, Morgan Lawrenz and Vijay S. Pande
Methods in Enzymology, 557, 551-572, 2015.

Markov State Models Provide Insights into Dynamic Modulation of Protein Function.

Stanford
Diwakar Shukla, Carlos X. Hernandez, Jeffrey K. Weber and Vijay S. Pande
Accounts of Chemical Research, 48 (2), 414–422, 2015.

Cloud computing approaches for predicting ligand-binding poses and pathways

Stanford
Morgan Lawrenz, Diwakar Shukla and Vijay S. Pande
Scientific Reports, 5, Article number: 7918, 2015. doi:10.1038/srep07918

Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics

Stanford
Matthew P. Harrigan, Diwakar Shukla and Vijay S. Pande
Journal of Chemical Theory and Computation, 11 (3), 1094–1101, 2015.

Activation pathway of Src kinase reveals intermediate states as targets for drug design.

Faculty of 1000 (F1000)Stanford
Diwakar Shukla, Yilin Meng, Benoit Roux and Vijay S. Pande
Nature Communications, 5, Article number: 3397 (2014) doi:10.1038/ncomms4397

Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.

Faculty of 1000 (F1000)Stanford
K. J. Kohlhoff*, D. Shukla*, M. Lawrenz*, G. R. Bowman, D. E. Konerding, D. Belov, R. B. Altman & V. S. Pande
Nature Chemistry 6, 15–21 (2014) doi:10.1038/nchem.1821 *denotes co-first author

Data-driven drug discovery: integration of multiple information sources to generate kinase inhibitor candidates

Stanford
Lili Peng, Morgan Lawrenz, Diwakar Shukla, Grace Tang, Vijay S. Pande and Russ B. Altman
bioRxiv, 2016

Automatic Order Parameters Selection In Markov State Models for Atomistic Understanding of Molecular Dynamics Data.

Stanford
Mohammad M. Sultan, Gert Kiss, Diwakar Shukla & Vijay S. Pande
Journal of Chemical Theory and Computation, 12, 10, 5217-5223, 2014.

Complex Pathways in Folding of Protein G Explored by Simulation and Experiment.

Stanford
Lisa J. Lapidus, Srabasti Acharya, Christian R. Schwantes, Ling Wu, Diwakar Shukla, Michael King, Stephen J. DeCamp & Vijay S. Pande
Biophysical Journal, 107, 4, 947-955, 2014.

To Milliseconds and Beyond: Challenges in the Simulation of Protein Folding.

Stanford
T. J. Lane, D. Shukla, K. A. Beauchamp & V. S. Pande
Current Opinion in Structural Biology, 23, 1, 58-65, (2013).

OpenMM 4.0: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.

Stanford
P. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, D. Shukla, T. Tye, M. Houston, T. Stich, C. Klein, M. R. Shirts, & V. S. Pande
Journal of Chemical Theory & Computation, 9, 1, 461-469, (2013).