Publications

[ A+ ] /[ A- ]

You can also view my GoogleScholar page here.

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation
    Gregory R Bowman
    Journal of Computational Chemistry 2016;37:558-566.
  8. Chapter Nine-How to Run FAST Simulations
    MI Zimmerman, GR Bowman
    Methods in Enzymology 2016;578:213-225.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. Extensive conformational heterogeneity within protein cores
    Gregory R Bowman, Phillip L Geissler
    The Journal of Physical Chemistry B 2014;118:6417-6423.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty
    Gregory R Bowman
    The Journal of Chemical Physics 2012;137:134111.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. Taming the complexity of protein folding
    Gregory R Bowman, Vincent A Voelz, Vijay S Pande
    Current Opinion in Structural Biology 2011;21:4-11.
  30. 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.
  31. 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.
  32. 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.
  33. 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.
  34. Protein folded states are kinetic hubs
    Gregory R Bowman, Vijay S Pande
    Proceedings of the National Academy of Sciences 2010;107:10890-10895.
  35. 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.
  36. 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.
  37. 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.
  38. 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.
  39. 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.
  40. 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.
  41. 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.
  42. 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.
  43. 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.
  44. The roles of entropy and kinetics in structure prediction
    Gregory R Bowman, Vijay S Pande
    PloS ONE 2009;4:e5840.
  45. 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.
  46. 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.
  47. 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.
  48. 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.
  49. 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.