Kyle A. Beauchamp
Kyle A. Beauchamp
Biophysics Program, Stanford University
Verified email at stanford.edu
Title
Cited by
Cited by
Year
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
9032015
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
7122017
Everything you wanted to know about Markov State Models but were afraid to ask
VS Pande, K Beauchamp, GR Bowman
Methods 52 (1), 99-105, 2010
5842010
Molecular simulation of ab initio protein folding for a millisecond folder NTL9 (1− 39)
VA Voelz, GR Bowman, K Beauchamp, VS Pande
Journal of the American Chemical Society 132 (5), 1526-1528, 2010
5532010
OpenMM 4: a reusable, extensible, hardware independent library for high performance molecular simulation
P Eastman, MS Friedrichs, JD Chodera, RJ Radmer, CM Bruns, JP Ku, ...
Journal of chemical theory and computation 9 (1), 461-469, 2013
5382013
Progress and challenges in the automated construction of Markov state models for full protein systems
GR Bowman, KA Beauchamp, G Boxer, VS Pande
The Journal of chemical physics 131, 124101, 2009
4072009
Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements
KA Beauchamp, YS Lin, R Das, VS Pande
American Chemical Society, 2012
4032012
Msmbuilder2: Modeling conformational dynamics at the picosecond to millisecond scale
KA Beauchamp, GR Bowman, TJ Lane, L Maibaum, IS Haque, VS Pande
Journal of Chemical Theory and Computation, 2011
3622011
To milliseconds and beyond: challenges in the simulation of protein folding
TJ Lane, D Shukla, KA Beauchamp, VS Pande
Current opinion in structural biology 23 (1), 58-65, 2013
3522013
MSMBuilder: statistical models for biomolecular dynamics
MP Harrigan, MM Sultan, CX Hernández, BE Husic, P Eastman, ...
Biophysical journal 112 (1), 10-15, 2017
1772017
Building a more predictive protein force field: a systematic and reproducible route to AMBER-FB15
LP Wang, KA McKiernan, J Gomes, KA Beauchamp, T Head-Gordon, ...
The Journal of Physical Chemistry B 121 (16), 4023-4039, 2017
1692017
Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories
TJ Lane, GR Bowman, KA Beauchamp, VA Voelz, VS Pande
Journal of the American Chemical Society, 2011
1632011
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
1542012
Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer
YS Lin, GR Bowman, KA Beauchamp, VS Pande
Biophysical journal 102 (2), 315-324, 2012
1212012
Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments
KA Beauchamp, DL Ensign, R Das, VS Pande
Proceedings of the National Academy of Sciences 108 (31), 12734, 2011
942011
Copernicus: A new paradigm for parallel adaptive molecular dynamics
S Pronk, P Larsson, I Pouya, GR Bowman, IS Haque, K Beauchamp, ...
Proceedings of 2011 International Conference for High Performance Computing …, 2011
792011
Escaping atom types in force fields using direct chemical perception
DL Mobley, CC Bannan, A Rizzi, CI Bayly, JD Chodera, VT Lim, NM Lim, ...
Journal of chemical theory and computation 14 (11), 6076-6092, 2018
752018
Orthogonal maximal abelian*-subalgebras of the 6× 6 matrices
K Beauchamp, R Nicoara
Linear algebra and its applications 428 (8-9), 1833-1853, 2008
572008
A molecular interpretation of 2D IR protein folding experiments with Markov state models
CR Baiz, YS Lin, CS Peng, KA Beauchamp, VA Voelz, VS Pande, ...
Biophysical journal 106 (6), 1359-1370, 2014
492014
Bayesian energy landscape tilting: towards concordant models of molecular ensembles
KA Beauchamp, VS Pande, R Das
Biophysical journal 106 (6), 1381-1390, 2014
492014
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Articles 1–20