Publications

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  1. Discovery of multiple hidden allosteric sites by combining Markov state models and experiments.
    Bowman GR, Bolin ER, Hart KM, Maguire BC, Marqusee S. Proc Natl Acad Sci USA. 2015 Mar 3;112(9):2734–9. PMCID: PMC4352775
  2. Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation.
    Bowman GR. J Comput Chem. 2015 Jun 16 DOI: 10.1002/jcc.23973.
  3. FAST conformational searches by balancing exploration/exploitation tradeoffs.
    Zimmerman M, Bowman GR. J Chem Theor Comp. 2015 Nov 11, in press.
  4. Tabtoxinine-β-lactam is a “stealth” β-lactam antibiotic that evades β-lactamase-mediated antibiotic resistance.
    Hart KM, Reck M, Bowman GR, Wencewicz TA. Med. Chem. Commun. 2015 Sep 16, in press.
  5. Fluctuations within Folded Proteins: Implications for Thermodynamic and Allosteric Regulation.
    DuBay KH, Bowman GR, Geissler PL. Acc Chem Res. 2015 Feb 17;48(4):150217095752005.
  6. Extensive Conformational Heterogeneity within Protein Cores.
    Bowman GR, Geissler PL. J Phys Chem B. 2014 Mar 12;118(24):6417-6423. PMCID: PMC4065209
  7. An introduction to markov state models and their application to long timescale molecular simulation.
    Bowman GR, Pande VS, Noé F, editors. New York: Springer; 2014.
  8. A tutorial on building markov state models with MSMBuilder and coarse-graining them with BACE.
    Bowman GR. Methods Mol. Biol. Totowa, NJ: Humana Press; 2014;1084(Chapter 8):141–58.
  9. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways.
    Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS. Nat Chem. 2014 Jan 1;6(1):15–21. PMCID: PMC3923464
  10. Quantitative comparison of alternative methods for coarse-graining biological networks.
    Bowman GR, Meng L, Huang X. J Chem Phys. 2013 Sept 28;139(12):121905–9. PMCID: PMC3724791
  11. Dynamics of an Intrinsically Disordered Protein Reveal Metastable Conformations That Potentially Seed Aggregation.
    Qiao Q, Bowman GR, Huang X. J Am Chem Soc. 2013 Oct 17;135(43):16092-16101. PMID: 24021023
  12. Hierarchical Nyström methods for constructing Markov state models for conformational dynamics.
    Yao Y, Cui RZ, Bowman GR, Silva D-A, Sun J, Huang X. J Chem Phys. 2013 May 7;138(17):174106. PMID: 23656113
  13. Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites.
    Bowman GR, Geissler PL. Proc Natl Acad Sci USA. 2012 Jul 17;109(29):11681–6. PMCID: PMC3406870
  14. Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty.
    Bowman GR. J Chem Phys. 2012 Oct 7;137(13):134111. PMCID: PMC3477182
  15. Exploiting a natural conformational switch to engineer an interleukin-2 ‘superkine’.
    Levin AM, Bates DL, Ring AM, Krieg C, Lin JT, Su L, Moraga I, Raeber ME, Bowman GR, Novick P, Pande VS, Fathman CG, Boyman O, Garcia KC. Nature. 2012 Apr 26;484(7395):529–33. PMCID: PMC3338870
  16. Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.
    Ring AM, Lin J, Feng D, Mitra S, Rickert M, Bowman GR, Pande VS, Li P, Moraga I, Spolski R, Özkan E, Leonard WJ, Garcia KC. Nat. Immunol. 2012 Oct 28;13(12):1187–95. PMCID: PMC3501574
  17. Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment.
    Voelz VA, Jager M, Yao S, Chen Y, Zhu L, Waldauer SA, Bowman GR, Friedrichs M, Bakajin O, Lapidus LJ, Weiss S, Pande VS. J Am Chem Soc. 2012 Jul 19;134(30):12565−12577. PMCID: PMC3462454
  18. Bridging the Gap Between Optical Spectroscopic Experiments and Computer Simulations for Fast Protein Folding Dynamics.
    Cui RZ, Silva DA, Song J, Bowman GR, Zhuang W, Huang X. Curr Phys Chem. 2012;2:45-58.
  19. Atomistic folding simulations of the five-helix bundle protein λ(6−85).
    Bowman GR, Voelz VA, Pande VS. J Am Chem Soc. 2011 Feb 2;133(4):664–7. PMCID: PMC3043158
  20. Taming the complexity of protein folding.
    Bowman GR, Voelz VA, Pande VS. Curr Opin Struct Biol. 2011 Feb 28;21(1):4–11. PMCID: PMC3042729
  21. A role for both conformational selection and induced fit in ligand binding by the LAO protein.
    Silva D-A, Bowman GR, Sosa-Peinado A, Huang X. PLoS Comput Biol. 2011 May 1;7(5):e1002054. PMCID: PMC3102756
  22. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale.
    Beauchamp KA, Bowman GR, Lane TJ, Maibaum L, Haque IS, Pande VS. J Chem Theor Comp. 2011 Oct 11;7(10):3412–9. PMCID: PMC3224091
  23. Markov state model reveals folding and functional dynamics in ultra-long MD trajectories.
    Lane TJ, Bowman GR, Beauchamp K, Voelz VA, Pande VS. J Am Chem Soc. 2011 Nov 16;133(45):18413–9. PMCID: PMC3227799
  24. Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer.
    Lin Y-S, Bowman GR, Beauchamp KA, Pande VS. Biophys J. 2012 Jan 18;102(2):315–24. PMCID: PMC3260686
  25. Copernicus: A new paradigm for parallel adaptive molecular dynamics.
    Pronk S, Larsson P, Pouya I, Bowman GR, Haque IS, Beauchamp KA, Hess B, Pande VS, Kasson PM, Lindahl E. In SC ’11: Proc Conf High Perf Computing, Networking, Storage and Analysis, New York, NY, USA, 2011. ACM. 

  26. Protein folded states are kinetic hubs.
    Bowman GR, Pande VS. Proc Natl Acad Sci USA. 2010 Jun 15;107(24):10890–5. PMCID: PMC2890711
  27. Enhanced modeling via network theory: adaptive sampling of Markov state models.
    Bowman GR, Ensign D, Pande V. J Chem Theor Comp. 2010 Feb 17;6(3):787–94. PMCID: PMC3637129
  28. Network models for molecular kinetics and their initial applications to human health.
    Bowman GR, Huang X, Pande VS. Cell Research. 2010 Apr 27;20(6):622–30. PMCID: PMC4441225
  29. Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9 (1− 39).
    Voelz VA, Bowman GR, Beauchamp K, Pande VS. J Am Chem Soc. 2010 Feb 10;132(5):1526–8. PMCID: PMC2835335
  30. Everything you wanted to know about Markov State Models but were afraid to ask.
    Pande VS, Beauchamp K, Bowman GR. Methods. 2010 Sep 30;52(1):99–105. PMCID: PMC2933958
  31. Constructing multi-resolution markov state models (MSMs) to elucidate RNA hairpin folding mechanisms.
    Huang X, Yao Y, Bowman GR, Sun J, Guibas LJ, Carlsson G, Pnade VS. Pac Symp Biocomput. 2010;15:228–39. PMCID: PMC4423759
  32. Progress and challenges in the automated construction of Markov state models for full protein systems.
    Bowman GR, Beauchamp KA, Boxer G, Pande VS. J Chem Phys. 2009 Sep 28;131(12):124101. PMCID: PMC2766407
  33. Using generalized ensemble simulations and Markov state models to identify conformational states.
    Bowman GR, Huang X, Pande VS. Methods. 2009 Oct 31;49(2):197–201. PMCID: PMC2753735
  34. Simulated tempering yields insight into the low-resolution Rosetta scoring functions.
    Bowman GR, Pande VS. Proteins. 2009 Feb 15;74(3):777–88. PMID: 18767152
  35. The roles of entropy and kinetics in structure prediction.
    Bowman GR, Pande VS. PLoS ONE. 2009 June 1;4(6):e5840. PMCID: PMC2688754
  36. Rapid equilibrium sampling initiated from nonequilibrium data.
    Huang X, Bowman GR, Bacallado S, Pande VS. Proc Natl Acad Sci USA. 2009 Nov 24;106(47):19765–9. PMCID: PMC2785240
  37. Probing the nanosecond dynamics of a designed three-stranded Beta-sheet with a massively parallel molecular dynamics simulation.
    Voelz VA, Luttmann E, Bowman GR, Pande VS. Int J Mol Sci 2009 Mar 10;10(3):1013-1030. PMCID: PMC2672016
  38. Topological methods for exploring low-density states in biomolecular folding pathways.
    Yao Y, Sun J, Huang X, Bowman GR, Singh G, Lesnick M, Guibas LJ, Pande VS, Carlsson G. J Chem Phys. 2009 Apr 14;130(14):144115. PMCID: PMC2719471
  39. Structural insight into RNA hairpin folding intermediates.
    Bowman GR, Huang X, Yao Y, Sun J, Carlsson G, Guibas LJ, Pande VS. J Am Chem Soc 2008 July 1;130(30):9676- 9678. PMCID: PMC2652247
  40. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.
    Huang X, Bowman GR, Pande VS. J Chem Phys. 2008 May 28;128(20):205106. PMCID: PMC2809694
  41. Microarray-based resequencing of multiple Bacillus anthracis isolates.
    Zwick ME, Mcafee F, Cutler DJ, Read TD, Ravel J, Bowman GR, Galloway DR, Mateczun A. Genome Biol 2005 Dec 17;6(1):R10. PMCID: PMC549062