User profiles for K. A. Beauchamp

Kyle A. Beauchamp

Stanford, Tempus,
Verified email at tempus.com
Cited by 10324

[HTML][HTML] OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

…, RT McGibbon, Y Zhao, KA Beauchamp… - PLoS computational …, 2017 - journals.plos.org
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It
allows users to easily add new features, including forces with novel functional forms, new …

[PDF][PDF] MDTraj: a modern open library for the analysis of molecular dynamics trajectories

RT McGibbon, KA Beauchamp, MP Harrigan, C Klein… - Biophysical journal, 2015 - cell.com
As molecular dynamics (MD) simulations continue to evolve into powerful computational
tools for studying complex biomolecular systems, the necessity of flexible and easy-to-use …

OpenMM 4: a reusable, extensible, hardware independent library for high performance molecular simulation

…, CM Bruns, JP Ku, KA Beauchamp… - Journal of chemical …, 2013 - ACS Publications
OpenMM is a software toolkit for performing molecular simulations on a range of high
performance computing architectures. It is based on a layered architecture: the lower layers …

Progress and challenges in the automated construction of Markov state models for full protein systems

GR Bowman, KA Beauchamp, G Boxer… - The Journal of chemical …, 2009 - pubs.aip.org
Markov state models (MSMs) are a powerful tool for modeling both the thermodynamics and
kinetics of molecular systems. In addition, they provide a rigorous means to combine …

Are protein force fields getting better? A systematic benchmark on 524 diverse NMR measurements

KA Beauchamp, YS Lin, R Das… - Journal of chemical …, 2012 - ACS Publications
Recent hardware and software advances have enabled simulation studies of protein systems
on biophysically relevant time scales, often revealing the need for improved force fields. …

To milliseconds and beyond: challenges in the simulation of protein folding

TJ Lane, D Shukla, KA Beauchamp… - Current opinion in …, 2013 - Elsevier
Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding have
long been considered a holy grail of computational biology. Due to the large system sizes …

MSMBuilder2: modeling conformational dynamics on the picosecond to millisecond scale

KA Beauchamp, GR Bowman, TJ Lane… - Journal of chemical …, 2011 - ACS Publications
Markov state models provide a framework for understanding the fundamental states and
rates in the conformational dynamics of biomolecules. We describe an improved protocol for …

Building a more predictive protein force field: a systematic and reproducible route to AMBER-FB15

…, KA McKiernan, J Gomes, KA Beauchamp… - The Journal of …, 2017 - ACS Publications
The increasing availability of high-quality experimental data and first-principles calculations
creates opportunities for developing more accurate empirical force fields for simulation of …

[PDF][PDF] MSMBuilder: statistical models for biomolecular dynamics

…, P Eastman, CR Schwantes, KA Beauchamp… - Biophysical journal, 2017 - cell.com
MSMBuilder is a software package for building statistical models of high-dimensional time-series
data. It is designed with a particular focus on the analysis of atomistic simulations of …

'Candidatus Xenohaliotis californiensis', a newly described pathogen of abalone, Haliotis spp., along the west coast of North America.

…, KB Andree, KA Beauchamp… - … of Systematic and …, 2000 - microbiologyresearch.org
Withering syndrome is a fatal disease of wild and cultured abalone, Haliotis spp., that inhabit
the west coast of North America. The aetiological agent of withering syndrome has recently …