Beauchamp, Kyle A.

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

Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang, L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., et al. (2017) · PLOS Computational Biology

Parallel Computing and Optimization TechniquesProtein Structure and Dynamics

Cited by 2,748

Everything you wanted to know about Markov State Models but were afraid to ask

Pande, V. S., Beauchamp, K., & Bowman, G. R. (2010) · Methods

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 698

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

Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S. (2013) · Current Opinion in Structural Biology

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 409

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

Bowman, G. R., Beauchamp, K. A., Boxer, G., & Pande, V. S. (2009) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 396

MSMBuilder2: Modeling Conformational Dynamics on the Picosecond to Millisecond Scale

Beauchamp, K. A., Bowman, G. R., Lane, T. J., Maibaum, L., Haque, I. S., & Pande, V. S. (2011) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 372

MSMBuilder: Statistical Models for Biomolecular Dynamics

Harrigan, M. P., Sultan, M. M., Hernández, C. X., Husic, B. E., Eastman, P., Schwantes, C. R., Beauchamp, K. A., McGibbon, R. T., & Pande, V. S. (2016) · Biophysical Journal

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 277

MSMBuilder: Statistical Models for Biomolecular Dynamics

Harrigan, M. P., Sultan, M. M., Hernández, C. X., Husic, B. E., Eastman, P., Schwantes, C. R., Beauchamp, K. A., McGibbon, R. T., & Pande, V. S. (2017) · Biophysical Journal

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 277

Simple few-state models reveal hidden complexity in protein folding

Beauchamp, K. A., McGibbon, R., Lin, Y.-S., & Pande, V. S. (2012) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 161

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

Lin, Y.-S., Bowman, G. R., Beauchamp, K. A., & Pande, V. S. (2012) · Biophysical Journal

Alzheimer's disease research and treatmentsProtein Structure and Dynamics

Cited by 111

Validation of an Expanded Carrier Screen that Optimizes Sensitivity via Full-Exon Sequencing and Panel-wide Copy Number Variant Identification

Hogan, G. J., Vysotskaia, V. S., Beauchamp, K. A., Seisenberger, S., Grauman, P. V., Haas, K. R., Hong, S. H., Jeon, D., Kash, S., Lai, H. H., et al. (2018) · Clinical Chemistry

Genomics and Rare DiseasesPrenatal Screening and Diagnostics

Cited by 71

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

Baiz, C. R., Lin, Y.-S., Peng, C. S., Beauchamp, K. A., Voelz, V. A., Pande, V. S., & Tokmakoff, A. (2014) · Biophysical Journal

Protein Structure and DynamicsSpectroscopy and Quantum Chemical Studies

Cited by 51

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

Shi, X., Beauchamp, K. A., Harbury, P. B., & Herschlag, D. (2014) · Proceedings of the National Academy of Sciences

DNA and Nucleic Acid ChemistryProtein Structure and Dynamics

Cited by 38