MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
McGibbon, Robert T., Beauchamp, Kyle A., Harrigan, Matthew P., Klein, Christoph, Swails, Jason M., Hernández, Carlos X., Schwantes, Christian R., Wang, Lee-Ping, Lane, Thomas J., Pande, Vijay S.
Published in Biophysical journal (20.10.2015)
Published in Biophysical journal (20.10.2015)
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Journal Article
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
Eastman, Peter, Swails, Jason, Chodera, John D, McGibbon, Robert T, Zhao, Yutong, Beauchamp, Kyle A, Wang, Lee-Ping, Simmonett, Andrew C, Harrigan, Matthew P, Stern, Chaya D, Wiewiora, Rafal P, Brooks, Bernard R, Pande, Vijay S
Published in PLoS computational biology (01.07.2017)
Published in PLoS computational biology (01.07.2017)
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Journal Article
MSMBuilder: Statistical Models for Biomolecular Dynamics
Harrigan, Matthew P., Sultan, Mohammad M., Hernández, Carlos X., Husic, Brooke E., Eastman, Peter, Schwantes, Christian R., Beauchamp, Kyle A., McGibbon, Robert T., Pande, Vijay S.
Published in Biophysical journal (10.01.2017)
Published in Biophysical journal (10.01.2017)
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Journal Article
Automated Discovery and Refinement of Reactive Molecular Dynamics Pathways
Wang, Lee-Ping, McGibbon, Robert T, Pande, Vijay S, Martinez, Todd J
Published in Journal of chemical theory and computation (09.02.2016)
Published in Journal of chemical theory and computation (09.02.2016)
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Journal Article
Quantum chemical benchmark databases of gold-standard dimer interaction energies
Donchev, Alexander G., Taube, Andrew G., Decolvenaere, Elizabeth, Hargus, Cory, McGibbon, Robert T., Law, Ka-Hei, Gregersen, Brent A., Li, Je-Luen, Palmo, Kim, Siva, Karthik, Bergdorf, Michael, Klepeis, John L., Shaw, David E.
Published in Scientific data (10.02.2021)
Published in Scientific data (10.02.2021)
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Journal Article
Statistical Model Selection for Markov Models of Biomolecular Dynamics
McGibbon, Robert T, Schwantes, Christian R, Pande, Vijay S
Published in The journal of physical chemistry. B (19.06.2014)
Published in The journal of physical chemistry. B (19.06.2014)
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Journal Article
Identification of simple reaction coordinates from complex dynamics
McGibbon, Robert T, Husic, Brooke E, Pande, Vijay S
Published in The Journal of chemical physics (28.01.2017)
Published in The Journal of chemical physics (28.01.2017)
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Journal Article
Improving the accuracy of Møller-Plesset perturbation theory with neural networks
McGibbon, Robert T., Taube, Andrew G., Donchev, Alexander G., Siva, Karthik, Hernández, Felipe, Hargus, Cory, Law, Ka-Hei, Klepeis, John L., Shaw, David E.
Published in The Journal of chemical physics (28.10.2017)
Published in The Journal of chemical physics (28.10.2017)
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Journal Article
Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics
McGibbon, Robert T, Pande, Vijay S
Published in Journal of chemical theory and computation (09.07.2013)
Published in Journal of chemical theory and computation (09.07.2013)
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Journal Article
SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, Pauli, Gommers, Ralf, Oliphant, Travis E., Haberland, Matt, Reddy, Tyler, Cournapeau, David, Burovski, Evgeni, Peterson, Pearu, Weckesser, Warren, Bright, Jonathan, van der Walt, Stéfan J., Brett, Matthew, Wilson, Joshua, Millman, K. Jarrod, Mayorov, Nikolay, Nelson, Andrew R. J., Jones, Eric, Kern, Robert, Larson, Eric, Carey, C J, Polat, İlhan, Feng, Yu, Moore, Eric W., VanderPlas, Jake, Laxalde, Denis, Perktold, Josef, Cimrman, Robert, Henriksen, Ian, Quintero, E. A., Harris, Charles R., Archibald, Anne M., Ribeiro, Antônio H., Pedregosa, Fabian, van Mulbregt, Paul
Published in Nature methods (01.03.2020)
Published in Nature methods (01.03.2020)
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Journal Article
Osprey: Hyperparameter Optimization for Machine Learning
T. McGibbon, Robert, X. Hernández, Carlos, P. Harrigan, Matthew, Kearnes, Steven, M. Sultan, Mohammad, Jastrzebski, Stanislaw, E. Husic, Brooke, S. Pande, Vijay
Published in Journal of open source software (07.09.2016)
Published in Journal of open source software (07.09.2016)
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Journal Article
Efficient hyperparameter optimization by way of PAC-Bayes bound minimization
Cherian, John J, Taube, Andrew G, McGibbon, Robert T, Angelikopoulos, Panagiotis, Blanc, Guy, Snarski, Michael, Richman, Daniel D, Klepeis, John L, Shaw, David E
Year of Publication 14.08.2020
Year of Publication 14.08.2020
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Journal Article
Identification of simple reaction coordinates from complex dynamics
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