User profiles for K. A. Beauchamp
Kyle A. BeauchampStanford, Tempus, Verified email at tempus.com Cited by 10324 |
[HTML][HTML] OpenMM 7: Rapid development of high performance algorithms for molecular dynamics
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 …
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
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 …
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
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 …
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 …
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
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. …
on biophysically relevant time scales, often revealing the need for improved force fields. …
To milliseconds and beyond: challenges in the simulation of protein folding
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 …
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
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 …
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
The increasing availability of high-quality experimental data and first-principles calculations
creates opportunities for developing more accurate empirical force fields for simulation of …
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 …
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 …
the west coast of North America. The aetiological agent of withering syndrome has recently …