Publications : Methods

SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes

Scientific Reports, 8(1), 2018
Chuankai Zhao 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

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

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

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

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

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

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

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

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