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Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2
Biophysical Journal, 110(8): 1716-1719, 2016
Christian~R. Schwantes and Diwakar Shukla and Vijay~S. Pande
Medicine
BibTeX
BibTeX
@article{Schwantes2016, doi = {10.1016/j.bpj.2016.03.026}, url = {https://doi.org/10.1016/j.bpj.2016.03.026}, year = {2016}, month = apr, publisher = {Elsevier {BV}}, volume = {110}, number = {8}, pages = {1716--1719}, author = {Christian~R. Schwantes and Diwakar Shukla and Vijay~S. Pande}, title = {Markov State Models and {tICA} Reveal a Nonnative Folding Nucleus in Simulations of {NuG}2}, journal = {Biophysical Journal}
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
Medicine
Methods
BibTeX
BibTeX
@article{peng2016application, title={Application of new informatics tools for identifying allosteric lead ligands of the c-Src kinase}, author={Peng, Lili X and Lawrenz, Morgan and Shukla, Diwakar and Tang, Grace W and Pande, Vijay S and Altman, Russ B}, journal={BioRxiv}, pages={038323}, year={2016}, publisher={Cold Spring Harbor Laboratory}
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
Medicine
Methods
BibTeX
BibTeX
@article{Meng2016Transition, doi = {10.1073/pnas.1602790113}, url = {https://doi.org/10.1073/pnas.1602790113}, year = {2016}, month = aug, publisher = {Proceedings of the National Academy of Sciences}, volume = {113}, number = {33}, pages = {9193--9198}, author = {Yilin Meng and Diwakar Shukla and Vijay S. Pande and Beno{\^{\i}}t Roux}, title = {Transition path theory analysis of c-Src kinase activation}, journal = {Proceedings of the National Academy of Sciences}
Conformational heterogeneity of the calmodulin binding interface
Nature Communications, 7(1), 2016
Diwakar Shukla and Ariana Peck and Vijay S. Pande
Medicine
BibTeX
BibTeX
@article{Shukla2016Conformational, doi = {10.1038/ncomms10910}, url = {https://doi.org/10.1038/ncomms10910}, year = {2016}, month = apr, publisher = {Springer Science and Business Media {LLC}}, volume = {7}, number = {1}, author = {Diwakar Shukla and Ariana Peck and Vijay S. Pande}, title = {Conformational heterogeneity of the calmodulin binding interface}, journal = {Nature Communications}
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
Medicine
Methods
BibTeX
BibTeX
@incollection{shukla2015elucidating, title={Elucidating ligand-modulated conformational landscape of GPCRs using cloud-computing approaches}, author={Shukla, Diwakar and Lawrenz, Morgan and Pande, Vijay S}, booktitle={Methods in Enzymology}, volume={557}, pages={551--572}, year={2015}, publisher={Elsevier}
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
Methods
BibTeX
BibTeX
@article{Weber2015, doi = {10.1073/pnas.1501804112}, url = {https://doi.org/10.1073/pnas.1501804112}, year = {2015}, month = aug, publisher = {Proceedings of the National Academy of Sciences}, volume = {112}, number = {33}, pages = {10377--10382}, author = {Jeffrey K. Weber and Diwakar Shukla and Vijay S. Pande}, title = {Heat dissipation guides activation in signaling proteins}, journal = {Proceedings of the National Academy of Sciences}
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
Methods
BibTeX
BibTeX
@article{Shukla2015Markov, doi = {10.1021/ar5002999}, url = {https://doi.org/10.1021/ar5002999}, year = {2015}, month = jan, publisher = {American Chemical Society ({ACS})}, volume = {48}, number = {2}, pages = {414--422}, author = {Diwakar Shukla and Carlos X. Hern{\'{a}}ndez and Jeffrey K. Weber and Vijay S. Pande}, title = {Markov State Models Provide Insights into Dynamic Modulation of Protein Function}, journal = {Accounts of Chemical Research}
A network of molecular switches controls the activation of the two-component response regulator NtrC
Nature Communications, 6(1), 2015
Dan K. Vanatta and Diwakar Shukla and Morgan Lawrenz and Vijay S. Pande
Medicine
BibTeX
BibTeX
@article{Vanatta2015Network, doi = {10.1038/ncomms8283}, url = {https://doi.org/10.1038/ncomms8283}, year = {2015}, month = jun, publisher = {Springer Science and Business Media {LLC}}, volume = {6}, number = {1}, author = {Dan K. Vanatta and Diwakar Shukla and Morgan Lawrenz and Vijay S. Pande}, title = {A network of molecular switches controls the activation of the two-component response regulator {NtrC}}, journal = {Nature Communications}
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
Methods
BibTeX
BibTeX
@article{Lawrenz2015Cloud, doi = {10.1038/srep07918}, url = {https://doi.org/10.1038/srep07918}, year = {2015}, month = jan, publisher = {Springer Science and Business Media {LLC}}, volume = {5}, number = {1}, author = {Morgan Lawrenz and Diwakar Shukla and Vijay S. Pande}, title = {Cloud computing approaches for prediction of ligand binding poses and pathways}, journal = {Scientific Reports}
Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics
Journal of Chemical Theory and Computation, 11(3): 1094-1101, 2015
Matthew P. Harrigan and Diwakar Shukla and Vijay S. Pande
Methods
BibTeX
BibTeX
@article{Harrigan2015, doi = {10.1021/ct5010017}, url = {https://doi.org/10.1021/ct5010017}, year = {2015}, month = feb, publisher = {American Chemical Society ({ACS})}, volume = {11}, number = {3}, pages = {1094--1101}, author = {Matthew P. Harrigan and Diwakar Shukla and Vijay S. Pande}, title = {Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics}, journal = {Journal of Chemical Theory and Computation}
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