Publications : Journal Article

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

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

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

Nature Communications, 5(1), 2014
Diwakar Shukla and Yilin Meng and Beno^it Roux and Vijay S. Pande

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

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

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

To milliseconds and beyond: challenges in the simulation of protein folding

Current Opinion in Structural Biology, 23(1): 58-65, 2013
Thomas J Lane and Diwakar Shukla and Kyle A Beauchamp and Vijay S Pande

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

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

Effects of Solute-Solute Interactions on Protein Stability Studied Using Various Counterions and Dendrimers

PLoS ONE, 6(11): e27665, 2011
Curtiss P. Schneider and Diwakar Shukla and Bernhardt L. Trout

Complex Interactions between Molecular Ions in Solution and Their Effect on Protein Stability

Journal of the American Chemical Society, 133(46): 18713-18718, 2011
Diwakar Shukla and Curtiss P. Schneider and Bernhardt L. Trout