Bowman, Gregory R.

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

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

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites

Bowman, G. R., & Geissler, P. L. (2012) · Proceedings of the National Academy of Sciences

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 279

SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

Jansen, J., Reimer, K. C., Nagai, J. S., Varghese, F. S., Overheul, G. J., de Beer, M., Roverts, R., Daviran, D., Fermin, L. A. S., Willemsen, B., et al. (2022) · Cell Stem Cell

COVID-19 Clinical Research StudiesSARS-CoV-2 and COVID-19 Research

Cited by 259

Dynamics of an Intrinsically Disordered Protein Reveal Metastable Conformations That Potentially Seed Aggregation

Qiao, Q., Bowman, G. R., & Huang, X. (2013) · Journal of the American Chemical Society

Protein Structure and DynamicsAlzheimer's disease research and treatments

Cited by 182

Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment

Voelz, V. A., Jäger, M., Yao, S., Chen, Y., Zhu, L., Waldauer, S. A., Bowman, G. R., Friedrichs, M., Bakajin, O., Lapidus, L. J., et al. (2012) · Journal of the American Chemical Society

Protein Structure and DynamicsRNA and protein synthesis mechanisms

Cited by 140

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

Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant

Pascolutti, R., Sun, X., Kao, J., Maute, R. L., Ring, A. M., Bowman, G. R., & Kruse, A. C. (2016) · Structure

Cancer Immunotherapy and BiomarkersProtein Structure and Dynamics

Cited by 102

Structural Insight into RNA Hairpin Folding Intermediates

Bowman, G. R., Huang, X., Yao, Y., Sun, J., Carlsson, G., Guibas, L. J., & Pande, V. S. (2008) · Journal of the American Chemical Society

RNA and protein synthesis mechanismsProtein Structure and Dynamics

Cited by 101

SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential

Vithani, N., Ward, M. D., Zimmerman, M. I., Novak, B., Borowsky, J. H., Singh, S., & Bowman, G. R. (2020) · Biophysical Journal

SARS-CoV-2 and COVID-19 ResearchProtein Structure and Dynamics

Cited by 84

SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential

Vithani, N., Ward, M. D., Zimmerman, M. I., Novak, B., Borowsky, J. H., Singh, S., & Bowman, G. R. (2021) · Biophysical Journal

SARS-CoV-2 and COVID-19 ResearchProtein Structure and Dynamics

Cited by 84

Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty

Bowman, G. R. (2012) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 76

Hierarchical Nyström methods for constructing Markov state models for conformational dynamics

Yao, Y., Cui, R. Z., Bowman, G. R., Silva, D.-A., Sun, J., & Huang, X. (2013) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 69

Quantitative comparison of alternative methods for coarse-graining biological networks

Bowman, G. R., Meng, L., & Huang, X. (2013) · The Journal of Chemical Physics

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 55

Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound forms

Stuchell-Brereton, M. D., Zimmerman, M. I., Miller, J. J., Mallimadugula, U. L., Incicco, J. J., Roy, D., Smith, L. G., Cubuk, J., Baban, B., DeKoster, G. T., et al. (2023) · Proceedings of the National Academy of Sciences

Alzheimer's disease research and treatmentsProtein Structure and Dynamics

Cited by 48

Extensive conformational heterogeneity within protein cores

Bowman, G. R., & Geissler, P. L. (2014) · The Journal of Physical Chemistry B

Protein Structure and DynamicsAdvanced Physical and Chemical Molecular Interactions

Cited by 38

Advancements in APOE and dementia research: Highlights from the 2023 AAIC Advancements: APOE conference

Kloske, C. M., Belloy, M. E., Blue, E. E., Bowman, G. R., Carrillo, M. C., Chen, X., Chiba‐Falek, O., Davis, A. A., Paolo, G. D., Garretti, F., et al. (2024) · Alzheimer's & Dementia

Alzheimer's disease research and treatmentsDementia and Cognitive Impairment Research

Cited by 33

Conformational distributions of isolated myosin motor domains encode their mechanochemical properties

Porter, J. R., Meller, A., Zimmerman, M. I., Greenberg, M. J., & Bowman, G. R. (2020) · eLife

Protein Structure and DynamicsCardiomyopathy and Myosin Studies

Cited by 31

Rapid and accurate prediction of protein homo-oligomer symmetry using Seq2Symm

Kshirsagar, M., Meller, A., Humphreys, I. R., Sledzieski, S., Xu, Y., Dodhia, R., Horvitz, E., Berger, B., Bowman, G. R., Ferres, J. L., et al. (2025) · Nature Communications

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 23

Rapid and accurate prediction of protein homo-oligomer symmetry with Seq2Symm

Kshirsagar, M., Meller, A., Humphreys, I., Sledzieski, S., Xu, Y., Dodhia, R., Horvitz, E., Berger, B., Bowman, G., Ferres, J. L., et al. (2024) · Nature Communications

Protein Structure and DynamicsMachine Learning in Bioinformatics

Cited by 22

Deep Mining of the Human Antibody Repertoire Identifies Frequent and Genetically Diverse CDRH3 Topologies Targetable by Vaccination

Habib, R., Solieva, S. O., Lin, Z. J., Ghosh, S., Bayruns, K., Singh, M., Agostino, C. J., Tursi, N. J., Sowers, K. J., Huang, J., et al. (2024) · Proceedings of the National Academy of Sciences

HIV Research and TreatmentMonoclonal and Polyclonal Antibodies Research

Cited by 8

How Well Can AI and Physics-Based Simulations Predict the Probability a Cryptic Pocket Is Open?

Zhang, S., Miller, J. J., & Bowman, G. R. (2026) · Journal of Chemical Theory and Computation

Protein Structure and DynamicsComputational Drug Discovery Methods

Cited by 7

Cooperative changes in solvent exposure identify cryptic pockets, conformational switches, and allosteric coupling

Porter, J. R., Moeder, K. E., Sibbald, C. A., Zimmerman, M. I., Hart, K. M., Greenberg, M. J., & Bowman, G. R. (2018) · Acta Crystallographica Section A Foundations and Advances

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 3