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Robert T. McGibbon
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MDTraj: a modern open library for the analysis of molecular dynamics trajectories
RT McGibbon, KA Beauchamp, MP Harrigan, C Klein, JM Swails, ...
Biophysical journal 109 (8), 1528-1532, 2015
11342015
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
P Eastman, J Swails, JD Chodera, RT McGibbon, Y Zhao, KA Beauchamp, ...
PLoS computational biology 13 (7), e1005659, 2017
10322017
Theano: A Python framework for fast computation of mathematical expressions
R Al-Rfou, G Alain, A Almahairi, C Angermueller, D Bahdanau, N Ballas, ...
arXiv e-prints, arXiv: 1605.02688, 2016
7952016
Discovering chemistry with an ab initio nanoreactor
LP Wang, A Titov, R McGibbon, F Liu, VS Pande, TJ Martínez
Nature chemistry 6 (12), 1044-1048, 2014
2742014
Electrocatalytic Carbon Dioxide Activation: The Rate‐Determining Step of Pyridinium‐Catalyzed CO2 Reduction
AJ Morris, RT McGibbon, AB Bocarsly
ChemSusChem 4 (2), 191-196, 2011
2112011
MSMBuilder: statistical models for biomolecular dynamics
MP Harrigan, MM Sultan, CX Hernández, BE Husic, P Eastman, ...
Biophysical journal 112 (1), 10-15, 2017
2072017
Theano: A Python framework for fast computation of mathematical expressions
TTD Team, R Al-Rfou, G Alain, A Almahairi, C Angermueller, D Bahdanau, ...
arXiv preprint arXiv:1605.02688, 2016
2072016
Variational cross-validation of slow dynamical modes in molecular kinetics
RT McGibbon, VS Pande
The Journal of chemical physics 142 (12), 03B621_1, 2015
1652015
Simple few-state models reveal hidden complexity in protein folding
KA Beauchamp, R McGibbon, YS Lin, VS Pande
Proceedings of the National Academy of Sciences 109 (44), 17807-17813, 2012
1632012
Automated discovery and refinement of reactive molecular dynamics pathways
LP Wang, RT McGibbon, VS Pande, TJ Martinez
Journal of chemical theory and computation 12 (2), 638-649, 2016
1002016
Perspective: Markov models for long-timescale biomolecular dynamics
CR Schwantes, RT McGibbon, VS Pande
The Journal of chemical physics 141 (9), 09B201_1, 2014
892014
Improving the accuracy of Mřller-Plesset perturbation theory with neural networks
RT McGibbon, AG Taube, AG Donchev, K Siva, F Hernández, C Hargus, ...
The Journal of chemical physics 147 (16), 161725, 2017
822017
Identification of simple reaction coordinates from complex dynamics
RT McGibbon, BE Husic, VS Pande
The Journal of Chemical Physics 146 (4), 044109, 2017
752017
Optimized parameter selection reveals trends in Markov state models for protein folding
BE Husic, RT McGibbon, MM Sultan, VS Pande
The Journal of chemical physics 145 (19), 194103, 2016
672016
Learning kinetic distance metrics for Markov state models of protein conformational dynamics
RT McGibbon, VS Pande
Journal of chemical theory and computation 9 (7), 2900-2906, 2013
532013
Osprey: Hyperparameter optimization for machine learning
RT McGibbon, CX Hernández, MP Harrigan, S Kearnes, MM Sultan, ...
Journal of Open Source Software 1 (5), 34, 2016
402016
Theano: A Python framework for fast computation of mathematical expressions. arXiv
R Al-Rfou, G Alain, A Almahairi, C Angermueller, D Bahdanau, N Ballas, ...
arXiv preprint arXiv:1605.02688, 2016
352016
Efficient maximum likelihood parameterization of continuous-time Markov processes
RT McGibbon, VS Pande
The Journal of chemical physics 143 (3), 034109, 2015
302015
Harm de Vries, David Warde-Farley, Dustin J
R Al-Rfou, G Alain, A Almahairi, C Angermueller, D Bahdanau, N Ballas, ...
Webb, Matthew Willson, Kelvin Xu, Lijun Xue, Li Yao, Saizheng Zhang, and …, 2016
282016
Statistical model selection for Markov models of biomolecular dynamics
RT McGibbon, CR Schwantes, VS Pande
The Journal of Physical Chemistry B 118 (24), 6475-6481, 2014
282014
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Articles 1–20