Publications : Methods

Shukla Group > Publications > Methods
Clear Filters
item thumbnail

Thirty years of molecular dynamics simulations on post-translational modifications of proteins

Physical Chemistry Chemical Physics, Volume 24, Pages  26371-26397, 2022.
Austin T Weigle, Jiangyan Feng and Diwakar Shukla*
Methods
Publisher's website BibTeX
item thumbnail

Multiagent Reinforcement Learning-Based Adaptive Sampling for Conformational Dynamics of Proteins

Journal of Chemical Theory and Computation, Volume 18, Issue 9, Pages 5422-5434, 2022.
Diego E. Kleiman and Diwakar Shukla*
Methods
Publisher's website BibTeX
item thumbnail

Active Learning of the Conformational Ensemble of Proteins using Maximum Entropy VAMPNets

bioRxiv, doi:10.1101/2023.01.12.523801
Diego E Kleiman and Diwakar Shukla
Methods
Publisher's website BibTeX
item thumbnail

Reconciling Membrane Protein Simulations with Experimental DEER Spectroscopy Data

Physical Chemistry Chemical Physics, In press, 2023.
Mittal, Shriyaa and Shukla, Diwakar
Methods
Publisher's website BibTeX
item thumbnail

Recent Advances in Machine Learning Variant Effect Prediction Tools for Protein Engineering

Industrial & Engineering Chemistry Research, Volume 61, Issue 19, Pages 6235–6245, 2022.
Jesse R. Horne and Diwakar Shukla
Methods
BibTeX
item thumbnail

Predicting the Activities of Drug Excipients on Biological Targets using One-Shot Learning

Journal of Physical Chemistry B, Volume 126, Issue 7, Pages 1492–1503, 2022.
Xuenan Mi and Diwakar Shukla
MedicineMethods
Publisher's website BibTeX
item thumbnail

Markov state modeling of membrane transport proteins.

Journal of Structural Biology, Volume 213, Issue 4, Article 107800, 2021.
Matthew C. Chan and Diwakar Shukla
MedicineMethods
Publisher's website BibTeX
item thumbnail

Impact of increased membrane realism on conformational sampling of proteins

Journal of Chemical Theory and Computation, Vol. 17, Issue 8, Pages 342–5357, 2021
Weigle, Austin T. and Carr, Matthew and Shukla, Diwakar
Plant BiologyMethods
Publisher's website BibTeX
item thumbnail

Structural Basis for Negative Regulation of ABA Signaling by ROP11 GTPase

bioRxiv, 2020
Zhao, Chuankai and Shukla, Diwakar
Plant BiologyMethods
Publisher's website BibTeX
item thumbnail

TLmutation: Predicting the Effects of Mutations Using Transfer Learning

The Journal of Physical Chemistry B, 124(19): 3845-3854, 2020
Shamsi, Zahra and Chan, Matthew and Shukla, Diwakar
Methods
Publisher's website BibTeX