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TLmutation: predicting the effects of mutations using transfer learning.

IllinoisMethods
Zahra Shamsi, Matthew Chan and Diwakar Shukla
In review, 2019.

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

IllinoisMethods
Chuankai Zhao and Diwakar Shukla
Scientific Reports, Volume 8, Article number: 17748, 2018.

Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy Experiments

IllinoisMethods
Shriyaa Mittal and Diwakar Shukla
Journal of Physical Chemistry B, Volume 122, Issue 48, Pages 10793–10805, 2018

REinforcement learning based Adaptive samPling: REAPing Rewards by Exploring Protein Conformational Landscapes

IllinoisMethods
Zahra Shamsi, Kevin J. Cheng and Diwakar Shukla
Journal of Physical Chemistry B, Volume 122, Issue 35, Pages 8386–8395, 2018.

Automatic Feature Selection in Markov State Models Using Genetic Algorithm.

IllinoisMethods
Qihua Chen#+, Jiangyan Feng+, Shriyaa Mittal and Diwakar Shukla. (#denotes undergraduate first-author, + denotes co-first author)
Journal of Computational Science Education, Volume 9, Issue 2, Pages 14-22, 2018.

Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings.

IllinoisMethods
Jiangyan Feng and Diwakar Shukla
The Journal of Physical Chemistry B, Volume 122, Issue 3, Pages 1017–1025, 2018.

Recruiting Machine Learning Methods for Molecular Simulations of Proteins

IllinoisMethods
Shriyaa Mittal and Diwakar Shukla
Molecular Simulation, Vol. 44, Issue 11, Pages 891-904, 2018.

Predicting Optimal DEER Label Positions to Study Protein Conformational Heterogeneity.

IllinoisMethods
Shriyaa Mittal and Diwakar Shukla
Journal of Physical Chemistry B, Volume 121, Issue 42, Pages 9761–9770, 2017.

Enhanced unbiased sampling of protein dynamics using evolutionary coupling information.

IllinoisMethods
Zahra Shamsi*, Alexander S. Moffett* and Diwakar Shukla. * indicates co-first author.
Scientific Reports, 7, Article number: 12700, 2017. doi:10.1038/s41598-017-12874-7

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

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

Heat Dissipation Guides Activation in Signaling Proteins

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

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

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

Cloud computing approaches for predicting ligand-binding poses and pathways

MethodsStanford
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

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

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

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

Molecular Computations of Preferential Interaction Coefficients of Proteins.

MethodsMIT
D. Shukla, C. Shinde and B. L. Trout
Journal of Physical Chemistry B, 113, 37, 12456-12554, 2009.