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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
BibTeX
BibTeX
@article{Feng2020, doi = {10.1021/acs.jpcb.9b11869}, url = {https://doi.org/10.1021/acs.jpcb.9b11869}, year = {2020}, month = apr, publisher = {American Chemical Society ({ACS})}, volume = {124}, number = {18}, pages = {3605--3615}, author = {Jiangyan Feng and Diwakar Shukla}, title = {{FingerprintContacts}: Predicting Alternative Conformations of Proteins from Coevolution}, journal = {The Journal of Physical Chemistry B}
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
BibTeX
BibTeX
@article{Mittal2018Maximizing, doi = {10.1021/acs.jpcb.8b07076}, url = {https://doi.org/10.1021/acs.jpcb.8b07076}, year = {2018}, month = oct, publisher = {American Chemical Society ({ACS})}, volume = {122}, number = {48}, pages = {10793--10805}, author = {Shriyaa Mittal and Diwakar Shukla}, title = {Maximizing Kinetic Information Gain of Markov State Models for Optimal Design of Spectroscopy Experiments}, journal = {The Journal of Physical Chemistry B}
Recruiting machine learning methods for molecular simulations of proteins
Molecular Simulation, 44(11): 891-904, 2018
Shriyaa Mittal and Diwakar Shukla
Methods
BibTeX
BibTeX
@article{Mittal2018Recruiting, doi = {10.1080/08927022.2018.1448976}, url = {https://doi.org/10.1080/08927022.2018.1448976}, year = {2018}, month = mar, publisher = {Informa {UK} Limited}, volume = {44}, number = {11}, pages = {891--904}, author = {Shriyaa Mittal and Diwakar Shukla}, title = {Recruiting machine learning methods for molecular simulations of proteins}, journal = {Molecular Simulation}
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
BibTeX
BibTeX
@article{Shamsi2018, doi = {10.1021/acs.jpcb.8b06521}, url = {https://doi.org/10.1021/acs.jpcb.8b06521}, year = {2018}, month = aug, publisher = {American Chemical Society ({ACS})}, volume = {122}, number = {35}, pages = {8386--8395}, author = {Zahra Shamsi and Kevin J. Cheng and Diwakar Shukla}, title = {Reinforcement Learning Based Adaptive Sampling: {REAPing} Rewards by Exploring Protein Conformational Landscapes}, journal = {The Journal of Physical Chemistry B}
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
BibTeX
BibTeX
@article{Feng2018, doi = {10.1021/acs.jpcb.7b07529}, url = {https://doi.org/10.1021/acs.jpcb.7b07529}, year = {2018}, month = jan, publisher = {American Chemical Society ({ACS})}, volume = {122}, number = {3}, pages = {1017--1025}, author = {Jiangyan Feng and Diwakar Shukla}, title = {Characterizing Conformational Dynamics of Proteins Using Evolutionary Couplings}, journal = {The Journal of Physical Chemistry B}
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
BibTeX
BibTeX
@article{chen2018automatic, title={Automatic Feature Selection in Markov State Models Using Genetic Algorithm}, author={Chen, Qihua and Feng, Jiangyan and Mittal, Shriyaa and Shukla, Diwakar}, year={2018}, month = feb, publisher = {}, volume = {9}, number = {2}, pages = {14--22}, journal = {Journal of Computational Science Education}
SAXS-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes
Scientific Reports, 8(1), 2018
Chuankai Zhao and Diwakar Shukla
Plant Biology
Methods
BibTeX
BibTeX
@article{Zhao2018SAXS, doi = {10.1038/s41598-018-36090-z}, url = {https://doi.org/10.1038/s41598-018-36090-z}, year = {2018}, month = dec, publisher = {Springer Science and Business Media {LLC}}, volume = {8}, number = {1}, author = {Chuankai Zhao and Diwakar Shukla}, title = {{SAXS}-guided Enhanced Unbiased Sampling for Structure Determination of Proteins and Complexes}, journal = {Scientific Reports}
Enhanced unbiased sampling of protein dynamics using evolutionary coupling information
Scientific Reports, 7(1), 2017
Zahra Shamsi and Alexander S. Moffett and Diwakar Shukla
Methods
BibTeX
BibTeX
@article{Shamsi2017Enhanced, doi = {10.1038/s41598-017-12874-7}, url = {https://doi.org/10.1038/s41598-017-12874-7}, year = {2017}, month = oct, publisher = {Springer Science and Business Media {LLC}}, volume = {7}, number = {1}, author = {Zahra Shamsi and Alexander S. Moffett and Diwakar Shukla}, title = {Enhanced unbiased sampling of protein dynamics using evolutionary coupling information}, journal = {Scientific Reports}
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
Methods
BibTeX
BibTeX
@article{Mittal2017Predicting, doi = {10.1021/acs.jpcb.7b04785}, url = {https://doi.org/10.1021/acs.jpcb.7b04785}, year = {2017}, month = aug, publisher = {American Chemical Society ({ACS})}, volume = {121}, number = {42}, pages = {9761--9770}, author = {Shriyaa Mittal and Diwakar Shukla}, title = {Predicting Optimal {DEER} Label Positions to Study Protein Conformational Heterogeneity}, journal = {The Journal of Physical Chemistry B}
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
Methods
BibTeX
BibTeX
@incollection{shukla2017application, title={Application of hidden Markov models in biomolecular simulations}, author={Shukla, Saurabh and Shamsi, Zahra and Moffett, Alexander S and Selvam, Balaji and Shukla, Diwakar}, booktitle={Hidden Markov Models}, pages={29--41}, year={2017}, publisher={Springer}
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