Publications : Journal Article

Molecular dynamics simulations reveal the conformational dynamics ofArabidopsis thalianaBRI1 and BAK1 receptor-like kinases

Journal of Biological Chemistry, 292(30): 12643-12652, 2017
Alexander S. Moffett and Kyle W. Bender and Steven C. Huber and Diwakar Shukla

Enhanced unbiased sampling of protein dynamics using evolutionary coupling information

Scientific Reports, 7(1), 2017
Zahra Shamsi and Alexander S. Moffett and Diwakar Shukla

Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform

Frontiers in Plant Science, 8, 2017
Amy Marshall-Colon and Stephen P. Long and Douglas K. Allen and Gabrielle Allen and Daniel A. Beard and Bedrich Benes and Susanne von Caemmerer and A. J. Christensen and Donna J. Cox and John C. Hart and Peter M. Hirst and Kavya Kannan and Daniel S. Katz and Jonathan P. Lynch and Andrew J. Millar and Balaji Panneerselvam and Nathan D. Price and Przemyslaw Prusinkiewicz and David Raila and Rachel G. Shekar and Stuti Shrivastava and Diwakar Shukla and Venkatraman Srinivasan and Mark Stitt and Matthew J. Turk and Eberhard O. Voit and Yu Wang and Xinyou Yin and Xin-Guang Zhu

Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2

Biophysical Journal, 110(8): 1716-1719, 2016
Christian~R. Schwantes and Diwakar Shukla and Vijay~S. Pande

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

Conformational heterogeneity of the calmodulin binding interface

Nature Communications, 7(1), 2016
Diwakar Shukla and Ariana Peck and Vijay S. Pande

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

A network of molecular switches controls the activation of the two-component response regulator NtrC

Nature Communications, 6(1), 2015
Dan K. Vanatta and Diwakar Shukla and Morgan Lawrenz and Vijay S. Pande

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

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