Publications : Methods

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Impact of increased membrane realism on conformational sampling of proteins

bioRxiv, 2021
Weigle, Austin T. and Carr, Matthew and Shukla, Diwakar
Plant BiologyMethods
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Reconciling Membrane Protein Simulations with Experimental DEER Spectroscopy Data

bioRxiv, 2020
Mittal, Shriyaa and Shukla, Diwakar
Methods
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Structural Basis for Negative Regulation of ABA Signaling by ROP11 GTPase

bioRxiv, 2020
Zhao, Chuankai and Shukla, Diwakar
Plant BiologyMethods
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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
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FingerprintContacts: Predicting Alternative Conformations of Proteins from Coevolution

The Journal of Physical Chemistry B, 124(18): 3605-3615, 2020
Jiangyan Feng and Diwakar Shukla
Methods
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Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy Experiments

The Journal of Physical Chemistry B, 122(48): 10793-10805, 2018
Shriyaa Mittal and Diwakar Shukla
Methods
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Recruiting machine learning methods for molecular simulations of proteins

Molecular Simulation, 44(11): 891-904, 2018
Shriyaa Mittal and Diwakar Shukla
Methods
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Reinforcement Learning Based Adaptive Sampling: REAPing Rewards by Exploring Protein Conformational Landscapes

The Journal of Physical Chemistry B, 122(35): 8386-8395, 2018
Zahra Shamsi and Kevin J. Cheng and Diwakar Shukla
Methods
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Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings

The Journal of Physical Chemistry B, 122(3): 1017-1025, 2018
Jiangyan Feng and Diwakar Shukla
Methods
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Automatic Feature Selection in Markov State Models Using Genetic Algorithm

Journal of Computational Science Education, 9(2): 14-22, 2018
Chen, Qihua and Feng, Jiangyan and Mittal, Shriyaa and Shukla, Diwakar
Methods
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