Publications

You can also view Greg’s GoogleScholar page here.

  1. Discovery of a cryptic allosteric site in Ebola’s ‘undruggable’ VP35 protein using simulations and experiments
    Matthew A. Cruz, Thomas E. Frederick, Sukrit Singh, Neha Vithani, Maxwell I. Zimmerman, Justin R. Porter, Katelyn E. Moeder, Gaya K. Amarasinghe, and Gregory R. Bowman https://doi.org/10.1101/2020.02.09.940510
  2. Conformational distributions of isolated myosin motor domains encode their mechanochemical properties
    Justin R. Porter, Artur Meller, Maxwell I. Zimmerman, Michael J. Greenberg, Gregory R. Bowman doi: https://doi.org/10.1101/2019.12.16.878264
  3. Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities
    Catherine R Knoverek, Gaya K Amarasinghe, Gregory R Bowman Trends in Biochemical Sciences, 2018;44:351-364
  4. Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding
    Xianqiang Sun, Sukrit Singh, Kendall J Blumer, Gregory R Bowman eLife 2018;7:e38465
    bioRxiv 2018:306647.
  5. Choice of adaptive sampling strategy impacts state discovery, transition probabilities, and the apparent mechanism of conformational changes
    Maxwell I Zimmerman, Justin R Porter, Xianqiang Sun, Roseane R Silva, Gregory R Bowman J. Chem. Theory, Comput. 2018, 14,11,5459-5475
    arXiv preprint arXiv:1805.04616 2018.
  6. Electron Cryo-microscopy Structure of Ebola Virus Nucleoprotein Reveals a Mechanism for Nucleocapsid-like Assembly
    Zhaoming Su, Chao Wu, Liuqing Shi, Priya Luthra, Grigore D Pintilie, Britney Johnson, Justin R Porter, Peng Ge, Muyuan Chen, Gai Liu, Thomas E Frederick, Jennifer M Binning, Gregory R Bowman, Z Hong Zhou, Christopher F Basler, Michael L Gross, Daisy W Leung, Wah Chiu, Gaya K Amarasinghe
    Cell 2018;172:966-978. e12.
  7. Enspara: Modeling molecular ensembles with scalable data structures and parallel computing
    Justin Porter, Maxwell I Zimmerman, Gregory R Bowman J. Chem. Phys. MMMK, 044108 (2019)
    bioRxiv 2018:431072.
  8. Exposons exploit cooperative changes in solvent exposure to detect cryptic allosteric sites and other functionally-relevant conformational transitions
    Justin R Porter, Katelyn E Moeder, Carrie A Sibbald, Maxwell I Zimmerman, Kathryn M Hart, Michael J Greenberg, Gregory R Bowman Biophysical Journal 116, 5, 2019, 818-830
    bioRxiv 2018:323568.
  9. Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models
    Maxwell I Zimmerman, Kathryn M Hart, Carrie A Sibbald, Thomas E Frederick, John R Jimah, Catherine R Knoverek, Niraj H Tolia, Gregory R Bowman
    ACS central science 2017;3:1311-1321.
  10. Quantifying allosteric communication via both concerted structural changes and conformational disorder with CARDS
    Sukrit Singh, Gregory R Bowman
    Journal of Chemical Theory and Computation 2017;13:1509-1517.
  11. Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators
    Kathryn M Hart, Katelyn E Moeder, Chris MW Ho, Maxwell I Zimmerman, Thomas E Frederick, Gregory R Bowman
    PloS ONE 2017;12:e0178678.
  12. Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer
    Guomin Shen, Weidong Cui, Hao Zhang, Fengbo Zhou, Wei Huang, Qian Liu, Yihu Yang, Shuang Li, Gregory R Bowman, J Evan Sadler, Michael L Gross, Weikai Li
    Nature Structural & Molecular Biology 2017;24:69-76.
  13. Endogenous retinoid X receptor ligands in mouse hematopoietic cells
    Haixia Niu, Hideji Fujiwara, Orsola di Martino, Gayla Hadwiger, Thomas E Frederick, María P Menéndez-Gutiérrez, Mercedes Ricote, Gregory R Bowman, John S Welch
    Sci. Signal. 2017;10:eaan1011.
  14. Mechanistic Basis for ATP-Dependent Inhibition of Glutamine Synthetase by Tabtoxinine-β-Lactam
    Garrett Patrick, Luting Fang, Jacob Schaefer, Sukrit Singh, Gregory Bowman, Timothy Adam Wencewicz
    Biochemistry 2017.
  15. Bladder-cancer-associated mutations in RXRA activate peroxisome proliferator-activated receptors to drive urothelial proliferation
    Angela M Halstead, Chiraag D Kapadia, Jennifer Bolzenius, Clarence E Chu, Andrew Schriefer, Lukas D Wartman, Gregory R Bowman, Vivek K Arora
    eLife 2017;6:e30862.
  16. Modelling proteins’ hidden conformations to predict antibiotic resistance
    Kathryn M Hart, Chris MW Ho, Supratik Dutta, Michael L Gross, Gregory R Bowman
    Nature Communications 2016;7:12965.
  17. Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation
    Gregory R Bowman
    Journal of Computational Chemistry 2016;37:558-566.
  18. Chapter Nine-How to Run FAST Simulations
    MI Zimmerman, GR Bowman
    Methods in Enzymology 2016;578:213-225.
  19. Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor
    Chris A Brosey, Chris Ho, Winnie Z Long, Sukrit Singh, Kathryn Burnett, Greg L Hura, Jay C Nix, Gregory R Bowman, Tom Ellenberger, John A Tainer
    Structure 2016;24:2067-2079.
  20. Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant
    Roberta Pascolutti, Xianqiang Sun, Joseph Kao, Roy L Maute, Aaron M Ring, Gregory R Bowman, Andrew C Kruse
    Structure 2016;24:1719-1728.
  21. FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs
    Maxwell I Zimmerman, Gregory R Bowman
    Journal of Chemical Theory and Computation 2015;11:5747-5757.
  22. Discovery of multiple hidden allosteric sites by combining Markov state models and experiments
    Gregory R Bowman, Eric R Bolin, Kathryn M Hart, Brendan C Maguire, Susan Marqusee
    Proceedings of the National Academy of Sciences 2015;112:2734-2739.
  23. Tabtoxinine-β-lactam is a “stealth” β-lactam antibiotic that evades β-lactamase-mediated antibiotic resistance
    Kathryn M Hart, Margaret Reck, Gregory R Bowman, Timothy A Wencewicz
    Med. Chem. Commun. 2015;7:118-127.
  24. Fluctuations within Folded Proteins: Implications for Thermodynamic and Allosteric Regulation
    Kateri H DuBay, Gregory R Bowman, Phillip L Geissler
    Accounts of Chemical Research 2015;48:1098-1105.
  25. Extensive conformational heterogeneity within protein cores
    Gregory R Bowman, Phillip L Geissler
    The Journal of Physical Chemistry B 2014;118:6417-6423.
  26. An introduction to markov state models and their application to long timescale molecular simulation
    Gregory R Bowman, Vijay S Pande, Frank Noé, editors. New York:
    Springer 2014.
  27. A tutorial on building Markov state models with MSMBuilder and coarse-graining them with BACE
    Gregory R Bowman
    Methods Mol. Biol. Totowa, NJ: Humana Press; 2014;1084(Chapter 8):141–58.
  28. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
    Kai J Kohlhoff, Diwakar Shukla, Morgan Lawrenz, Gregory R Bowman, David E Konerding, Dan Belov, Russ B Altman, Vijay S Pande
    Nature Chemistry 2014;6:15-21.
  29. Quantitative comparison of alternative methods for coarse-graining biological networks
    Gregory R Bowman, Luming Meng, Xuhui Huang
    The Journal of Chemical Physics 2013;139:121905.
  30. Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation
    Qin Qiao, Gregory R Bowman, Xuhui Huang
    Journal of the American Chemical Society 2013;135:16092-16101.
  31. Hierarchical Nyström methods for constructing Markov state models for conformational dynamics
    Yuan Yao, Raymond Z Cui, Gregory R Bowman, Daniel-Adriano Silva, Jian Sun, Xuhui Huang
    The Journal of Chemical Physics 2013;138:174106.
  32. Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites
    Gregory R Bowman, Phillip L Geissler
    Proceedings of the National Academy of Sciences 2012;109:11681-11686.
  33. Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty
    Gregory R Bowman
    The Journal of Chemical Physics 2012;137:134111.
  34. Exploiting a natural conformational switch to engineer an interleukin-2/superkine/’
    Aron M Levin, Darren L Bates, Aaron M Ring, Carsten Krieg, Jack T Lin, Leon Su, Ignacio Moraga, Miro E Raeber, Gregory R Bowman, Paul Novick, Vijay S Pande, C Garrison Fathman, Onur Boyman, K Christopher Garcia
    Nature 2012;484:529-533.
  35. Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15
    Aaron M Ring, Jian-Xin Lin, Dan Feng, Suman Mitra, Mathias Rickert, Gregory R Bowman, Vijay S Pande, Peng Li, Ignacio Moraga, Rosanne Spolski, Engin Özkan, Warren J Leonard, K Christopher Garcia
    Nature Immunology 2012;13:1187-1195.
  36. Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment
    Vincent A Voelz, Marcus Jäger, Shuhuai Yao, Yujie Chen, Li Zhu, Steven A Waldauer, Gregory R Bowman, Mark Friedrichs, Olgica Bakajin, Lisa J Lapidus, Shimon Weiss, Vijay S Pande
    Journal of the American Chemical Society 2012;134:12565-12577.
  37. Bridging the Gap Between Optical Spectroscopic Experiments and Computer Simulations for Fast Protein Folding Dynamics
    Raymond Z Cui, Daniel-Adriano Silva, Jian Song, Gregory R Bowman, Wei Zhuang, Xuhui Huang
    Curr Phys Chem. 2012;2:45-58.
  38. Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer
    Yu-Shan Lin, Gregory R Bowman, Kyle A Beauchamp, Vijay S Pande
    Biophysical Journal 2012;102:315.
  39. Taming the complexity of protein folding
    Gregory R Bowman, Vincent A Voelz, Vijay S Pande
    Current Opinion in Structural Biology 2011;21:4-11.
  40. A role for both conformational selection and induced fit in ligand binding by the LAO protein
    Daniel-Adriano Silva, Gregory R Bowman, Alejandro Sosa-Peinado, Xuhui Huang
    PLoS Comput Biol 2011;7:e1002054.
  41. MSMBuilder2: modeling conformational dynamics on the picosecond to millisecond scale
    Kyle A Beauchamp, Gregory R Bowman, Thomas J Lane, Lutz Maibaum, Imran S Haque, Vijay S Pande
    Journal of Chemical Theory and Computation 2011;7:3412-3419.
  42. Markov state model reveals folding and functional dynamics in ultra-long MD trajectories
    Thomas J Lane, Gregory R Bowman, Kyle Beauchamp, Vincent A Voelz, Vijay S Pande
    Journal of the American Chemical Society 2011;133:18413-18419.
  43. Copernicus: a new paradigm for parallel adaptive molecular dynamics
    Sander Pronk, Per Larsson, Iman Pouya, Gregory R Bowman, Imran S Haque, Kyle Beauchamp, Berk Hess, Vijay S Pande, Peter M Kasson, Erik Lindahl
    In SC ’11: Proc Conf High Perf Computing, Networking, Storage and Analysis, New York, NY, USA, 2011. ACM.
  44. Protein folded states are kinetic hubs
    Gregory R Bowman, Vijay S Pande
    Proceedings of the National Academy of Sciences 2010;107:10890-10895.
  45. Atomistic folding simulations of the five-helix bundle protein λ6− 85
    Gregory R Bowman, Vincent A Voelz, Vijay S Pande
    Journal of the American Chemical Society 2010;133:664-667.
  46. Enhanced modeling via network theory: Adaptive sampling of markov state models
    Gregory R Bowman, Daniel L Ensign, Vijay S Pande
    Journal of Chemical Theory and Computation 2010;6:787-794.
  47. Network models for molecular kinetics and their initial applications to human health
    Gregory R Bowman, Xuhui Huang, Vijay S Pande
    Cell Research 2010;20:622-630.
  48. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1− 39)
    Vincent A Voelz, Gregory R Bowman, Kyle Beauchamp, Vijay S Pande
    Journal of the American Chemical Society 2010;132:1526-1528.
  49. Everything you wanted to know about Markov State Models but were afraid to ask
    Vijay S Pande, Kyle Beauchamp, Gregory R Bowman
    Methods 2010;52:99-105.
  50. Constructing multi-resolution Markov state models (MSMs) to elucidate RNA hairpin folding mechanisms
    Xuhui Huang, Yuan Yao, Gregory R Bowman, Jian Sun, Leonidas J Guibas, Gunnar Carlsson, Vijay S Pande
    Pac Symp Biocomput. 2010;15:228–39.
  51. Progress and challenges in the automated construction of Markov state models for full protein systems
    Gregory R Bowman, Kyle A Beauchamp, George Boxer, Vijay S Pande
    The Journal of Chemical Physics 2009;131:124101.
  52. Using generalized ensemble simulations and Markov state models to identify conformational states
    Gregory R Bowman, Xuhui Huang, Vijay S Pande
    Methods 2009;49:197-201.
  53. Simulated tempering yields insight into the low‐resolution Rosetta scoring functions
    Gregory R Bowman, Vijay S Pande
    Proteins: Structure, Function, and Bioinformatics 2009;74:777-788.
  54. The roles of entropy and kinetics in structure prediction
    Gregory R Bowman, Vijay S Pande
    PloS ONE 2009;4:e5840.
  55. Rapid equilibrium sampling initiated from nonequilibrium data
    Xuhui Huang, Gregory R Bowman, Sergio Bacallado, Vijay S Pande
    Proceedings of the National Academy of Sciences 2009;106:19765-19769.
  56. Probing the nanosecond dynamics of a designed three-stranded Beta-sheet with a massively parallel molecular dynamics simulation
    Vincent A Voelz, Edgar Luttmann, Gregory R Bowman, Vijay S Pande
    International Journal of Molecular Sciences 2009;10:1013-1030.
  57. Topological methods for exploring low-density states in biomolecular folding pathways
    Yuan Yao, Jian Sun, Xuhui Huang, Gregory R Bowman, Gurjeet Singh, Michael Lesnick, Leonidas J Guibas, Vijay S Pande, Gunnar Carlsson
    The Journal of Chemical Physics 2009;130:144115.
  58. Structural insight into RNA hairpin folding intermediates
    Gregory R Bowman, Xuhui Huang, Yuan Yao, Jian Sun, Gunnar Carlsson, Leonidas J Guibas, Vijay S Pande
    Journal of the American Chemical Society 2008;130:9676-9678.
  59. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment
    Xuhui Huang, Gregory R Bowman, Vijay S Pande
    The Journal of Chemical Physics 2008;128:205106.