Bayesian Energy Landscape Tilting: Towards Concordant Models of Molecular Ensembles

Por Beauchamp, Kyle A., Pande, Vijay S., Das, Rhiju
Publicado em 2014

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

Por Bowman, Gregory R., Beauchamp, Kyle A., Boxer, George, Pande, Vijay S.
Publicado em 2009

Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments

Por Beauchamp, Kyle A., Ensign, Daniel L., Das, Rhiju, Pande, Vijay S.
Publicado em 2011

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

Por Beauchamp, Kyle A., Lin, Yu-Shan, Das, Rhiju, Pande, Vijay S.
Publicado em 2012

To Milliseconds and Beyond: Challenges in the Simulation of Protein Folding

Por Lane, Thomas J., Shukla, Diwakar, Beauchamp, Kyle A., Pande, Vijay S.
Publicado em 2012

From a structural average to the conformational ensemble of a DNA bulge

Por Shi, Xuesong, Beauchamp, Kyle A., Harbury, Pehr B., Herschlag, Daniel
Publicado em 2014

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer

Por Lin, Yu-Shan, Bowman, Gregory R., Beauchamp, Kyle A., Pande, Vijay S.
Publicado em 2012

Simple few-state models reveal hidden complexity in protein folding

Por Beauchamp, Kyle A., McGibbon, Robert, Lin, Yu-Shan, Pande, Vijay S.
Publicado em 2012

Probing the origins of two-state folding

Por Lane, Thomas J., Schwantes, Christian R., Beauchamp, Kyle A., Pande, Vijay S.
Publicado em 2013

MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale

Por Beauchamp, Kyle A., Bowman, Gregory R., Lane, Thomas J., Maibaum, Lutz, Haque, Imran S., Pande, Vijay S.
Publicado em 2011

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale

Por Parton, Daniel L., Grinaway, Patrick B., Hanson, Sonya M., Beauchamp, Kyle A., Chodera, John D.
Publicado no PLoS Comput Biol (2016)

Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive

Por Beauchamp, Kyle A., Behr, Julie M., Rustenburg, Ariën S., Bayly, Christopher I., Kroenlein, Kenneth, Chodera, John D.
Publicado no J Phys Chem B (2015)

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems

Por Fass, Josh, Sivak, David A., Crooks, Gavin E., Beauchamp, Kyle A., Leimkuhler, Benedict, Chodera, John D.
Publicado no Entropy (Basel) (2018)

A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models

Por Baiz, Carlos R., Lin, Yu-Shan, Peng, Chunte Sam, Beauchamp, Kyle A., Voelz, Vincent A., Pande, Vijay S., Tokmakoff, Andrei
Publicado em 2014

MSMBuilder: Statistical Models for Biomolecular Dynamics

Por Harrigan, Matthew P., Sultan, Mohammad M., Hernández, Carlos X., Husic, Brooke E., Eastman, Peter, Schwantes, Christian R., Beauchamp, Kyle A., McGibbon, Robert T., Pande, Vijay S.
Publicado no Biophys J (2017)

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

Por McGibbon, Robert T., Beauchamp, Kyle A., Harrigan, Matthew P., Klein, Christoph, Swails, Jason M., Hernández, Carlos X., Schwantes, Christian R., Wang, Lee-Ping, Lane, Thomas J., Pande, Vijay S.
Publicado no Biophys J (2015)

Escaping atom types in force fields using direct chemical perception

Por Mobley, David L., Bannan, Caitlin C., Rizzi, Andrea, Bayly, Christopher I., Chodera, John D., Lim, Victoria T., Lim, Nathan M., Beauchamp, Kyle A., Slochower, David R., Shirts, Michael R., Gilson, Michael K., Eastman, Peter K.
Publicado no J Chem Theory Comput (2018)

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

Por Eastman, Peter, Swails, Jason, Chodera, John D., McGibbon, Robert T., Zhao, Yutong, Beauchamp, Kyle A., Wang, Lee-Ping, Simmonett, Andrew C., Harrigan, Matthew P., Stern, Chaya D., Wiewiora, Rafal P., Brooks, Bernard R., Pande, Vijay S.
Publicado no PLoS Comput Biol (2017)

Systematic design and comparison of expanded carrier screening panels

Por Beauchamp, Kyle A, Muzzey, Dale, Wong, Kenny K, Hogan, Gregory J, Karimi, Kambiz, Candille, Sophie I, Mehta, Nikita, Mar-Heyming, Rebecca, Kaseniit, K Eerik, Kang, H Peter, Evans, Eric A, Goldberg, James D, Lazarin, Gabriel A, Haque, Imran S
Publicado no Genet Med (2018)

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

Por Eastman, Peter, Friedrichs, Mark S., Chodera, John D., Radmer, Randall J., Bruns, Christopher M., Ku, Joy P., Beauchamp, Kyle A., Lane, Thomas J., Wang, Lee-Ping, Shukla, Diwakar, Tye, Tony, Houston, Mike, Stich, Timo, Klein, Christoph, Shirts, Michael R., Pande, Vijay S.
Publicado em 2012