Kyle A. Beauchamp
Kyle A. Beauchamp
Other namesKyle Beauchamp
Stanford, Tempus,
Verified email at
Cited by
Cited by
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
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
Bioconda: sustainable and comprehensive software distribution for the life sciences
B Grüning, R Dale, A Sjödin, BA Chapman, J Rowe, CH Tomkins-Tinch, ...
Nature methods 15 (7), 475-476, 2018
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
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
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
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
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
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
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
MSMBuilder: statistical models for biomolecular dynamics
MP Harrigan, MM Sultan, CX Hernández, BE Husic, P Eastman, ...
Biophysical journal 112 (1), 10-15, 2017
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
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
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
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
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
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
Clinical utility of expanded carrier screening: results-guided actionability and outcomes
KAJ Taber, KA Beauchamp, GA Lazarin, D Muzzey, A Arjunan, ...
Genetics in Medicine 21 (5), 1041-1048, 2019
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
Validation of an expanded carrier screen that optimizes sensitivity via full-exon sequencing and panel-wide copy number variant identification
GJ Hogan, VS Vysotskaia, KA Beauchamp, S Seisenberger, PV Grauman, ...
Clinical chemistry 64 (7), 1063-1073, 2018
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