Gregory R. Bowman - Publications

Affiliations: 
2010- Biochemistry and Molecular Biophysics Washington University, Saint Louis, St. Louis, MO 

51 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Sun X, Singh S, Blumer K, Bowman GR. Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding. Elife. 7. PMID 30289386 DOI: 10.7554/eLife.38465  1
2018 Zimmerman MI, Porter JR, Sun X, Silva RR, Bowman G. Choice of adaptive sampling strategy impacts state discovery, transition probabilities, and the apparent mechanism of conformational changes. Journal of Chemical Theory and Computation. PMID 30240203 DOI: 10.1021/acs.jctc.8b00500  0.36
2017 Patrick G, Fang L, Schaefer J, Singh S, Bowman G, Wencewicz TA. Mechanistic Basis for ATP-Dependent Inhibition of Glutamine Synthetase by Tabtoxinine-β-Lactam. Biochemistry. PMID 29039929 DOI: 10.1021/acs.biochem.7b00838  1
2017 Singh S, Bowman GR. Quantifying allosteric communication via both concerted structural changes and conformational disorder with CARDS. Journal of Chemical Theory and Computation. PMID 28282132 DOI: 10.1021/acs.jctc.6b01181  1
2017 Sun X, Laroche G, Wang X, Ågren H, Bowman G, M Giguère P, Tu Y. Propagation of the allosteric modulation induced by sodium in the δ opioid receptor. Chemistry (Weinheim An Der Bergstrasse, Germany). PMID 28182309 DOI: 10.1002/chem.201605575  0.36
2016 Brosey CA, Ho C, Long WZ, Singh S, Burnett K, Hura GL, Nix JC, Bowman GR, Ellenberger T, Tainer JA. Defining NADH-Driven Allostery Regulating Apoptosis-Inducing Factor. Structure (London, England : 1993). PMID 27818101 DOI: 10.1016/j.str.2016.09.012  1
2016 Hart KM, Ho CM, Dutta S, Gross ML, Bowman GR. Modelling proteins' hidden conformations to predict antibiotic resistance. Nature Communications. 7: 12965. PMID 27708258 DOI: 10.1038/ncomms12965  1
2016 Pascolutti R, Sun X, Kao J, Maute RL, Ring AM, Bowman GR, Kruse AC. Structure and Dynamics of PD-L1 and an Ultra-High-Affinity PD-1 Receptor Mutant. Structure (London, England : 1993). PMID 27618663 DOI: 10.1016/j.str.2016.06.026  1
2016 Hart KM, Reck M, Bowman GR, Wencewicz TA. Tabtoxinine-β-lactam is a "stealth" β-lactam antibiotic that evades β-lactamase-mediated antibiotic resistance Medchemcomm. 7: 118-127. DOI: 10.1039/c5md00325c  1
2015 Zimmerman MI, Bowman GR. FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs. Journal of Chemical Theory and Computation. PMID 26588361 DOI: 10.1021/acs.jctc.5b00737  1
2015 Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS. Corrigendum: Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nature Chemistry. 7: 759. PMID 26291949 DOI: 10.1038/nchem.2272  1
2015 Bowman GR. Accurately modeling nanosecond protein dynamics requires at least microseconds of simulation. Journal of Computational Chemistry. PMID 26077712 DOI: 10.1002/jcc.23973  1
2015 Bowman GR, Bolin ER, Hart KM, Maguire BC, Marqusee S. Discovery of multiple hidden allosteric sites by combining Markov state models and experiments. Proceedings of the National Academy of Sciences of the United States of America. 112: 2734-9. PMID 25730859 DOI: 10.1073/pnas.1417811112  1
2014 Bowman GR, Geissler PL. Extensive conformational heterogeneity within protein cores Journal of Physical Chemistry B. 118: 6417-6423. PMID 24564338 DOI: 10.1021/jp4105823  1
2014 Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS. Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways Nature Chemistry. 6: 15-21. PMID 24345941 DOI: 10.1038/nchem.1821  1
2014 Bowman GR, Noé F. Software for building Markov state models. Advances in Experimental Medicine and Biology. 797: 139. PMID 24297281 DOI: 10.1007/978-94-007-7606-7_11  1
2014 Bowman GR. An overview and practical guide to building Markov state models. Advances in Experimental Medicine and Biology. 797: 7-22. PMID 24297272 DOI: 10.1007/978-94-007-7606-7_2  1
2014 Bowman GR, Pande VS, Noé F. Introduction and overview of this book Advances in Experimental Medicine and Biology. 797: 1-6. PMID 24297271 DOI: 10.1007/978-94-007-7606-7-1  1
2014 Bowman GR. A tutorial on building markov state models with MSMBuilder and coarse-graining them with BACE. Methods in Molecular Biology (Clifton, N.J.). 1084: 141-58. PMID 24061920 DOI: 10.1007/978-1-62703-658-0_8  1
2013 Bowman GR, Meng L, Huang X. Quantitative comparison of alternative methods for coarse-graining biological networks. The Journal of Chemical Physics. 139: 121905. PMID 24089717 DOI: 10.1063/1.4812768  1
2013 Qiao Q, Bowman GR, Huang X. Dynamics of an intrinsically disordered protein reveal metastable conformations that potentially seed aggregation. Journal of the American Chemical Society. 135: 16092-101. PMID 24021023 DOI: 10.1021/ja403147m  1
2013 Yao Y, Cui RZ, Bowman GR, Silva DA, Sun J, Huang X. Hierarchical Nyström methods for constructing Markov state models for conformational dynamics. The Journal of Chemical Physics. 138: 174106. PMID 23656113 DOI: 10.1063/1.4802007  1
2012 Ring AM, Lin JX, Feng D, Mitra S, Rickert M, Bowman GR, Pande VS, Li P, Moraga I, Spolski R, Ozkan E, Leonard WJ, Garcia KC. Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15. Nature Immunology. 13: 1187-95. PMID 23104097 DOI: 10.1038/ni.2449  1
2012 Bowman GR. Improved coarse-graining of Markov state models via explicit consideration of statistical uncertainty. The Journal of Chemical Physics. 137: 134111. PMID 23039589 DOI: 10.1063/1.4755751  1
2012 Bowman GR, Geissler PL. Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites Proceedings of the National Academy of Sciences of the United States of America. 109: 11681-11686. PMID 22753506 DOI: 10.1073/pnas.1209309109  1
2012 Voelz VA, Jäger M, Yao S, Chen Y, Zhu L, Waldauer SA, Bowman GR, Friedrichs M, Bakajin O, Lapidus LJ, Weiss S, Pande VS. Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. Journal of the American Chemical Society. 134: 12565-77. PMID 22747188 DOI: 10.1021/ja302528z  1
2012 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. Exploiting a natural conformational switch to engineer an interleukin-2 'superkine'. Nature. 484: 529-33. PMID 22446627 DOI: 10.1038/nature10975  1
2012 Lin YS, Bowman GR, Beauchamp KA, Pande VS. Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer Biophysical Journal. 102: 315-324. PMID 22339868 DOI: 10.1016/j.bpj.2011.12.002  1
2011 Beauchamp KA, Bowman GR, Lane TJ, Maibaum L, Haque IS, Pande VS. MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. Journal of Chemical Theory and Computation. 7: 3412-3419. PMID 22125474 DOI: 10.1021/ct200463m  1
2011 Lane TJ, Bowman GR, Beauchamp K, Voelz VA, Pande VS. Markov State model reveals folding and functional dynamics in ultra-long MD trajectories Journal of the American Chemical Society. 133: 18413-18419. PMID 21988563 DOI: 10.1021/ja207470h  1
2011 Silva DA, Bowman GR, Sosa-Peinado A, Huang X. A role for both conformational selection and induced fit in ligand binding by the LAO protein. Plos Computational Biology. 7: e1002054. PMID 21637799 DOI: 10.1371/journal.pcbi.1002054  1
2011 Bowman GR, Voelz VA, Pande VS. Atomistic folding simulations of the five-helix bundle protein λ 6-85 Journal of the American Chemical Society. 133: 664-667. PMID 21174461 DOI: 10.1021/ja106936n  1
2011 Bowman GR, Voelz VA, Pande VS. Taming the complexity of protein folding Current Opinion in Structural Biology. 21: 4-11. PMID 21081274 DOI: 10.1016/j.sbi.2010.10.006  1
2011 Pronk S, Larsson P, Pouya I, Bowman GR, Haque IS, Beauchamp K, Hess B, Pande VS, Kasson PM, Lindahl E. Copernicus: A new paradigm for parallel adaptive molecular dynamics Proceedings of 2011 Sc - International Conference For High Performance Computing, Networking, Storage and Analysis. DOI: 10.1145/2063384.2063465  1
2011 Beauchamp KA, Bowman GR, Lane TJ, Maibaum L, Haque IS, Pande VS. MSMBuilder2: Modeling conformational dynamics on the picosecond to millisecond scale Journal of Chemical Theory and Computation. 7: 3412-3419. DOI: 10.1021/ct200463m  1
2010 Bowman GR, Ensign DL, Pande VS. Enhanced modeling via network theory: Adaptive sampling of Markov state models. Journal of Chemical Theory and Computation. 6: 787-794. PMID 23626502 DOI: 10.1021/ct900620b  1
2010 Pande VS, Beauchamp K, Bowman GR. Everything you wanted to know about Markov State Models but were afraid to ask. Methods (San Diego, Calif.). 52: 99-105. PMID 20570730 DOI: 10.1016/j.ymeth.2010.06.002  1
2010 Bowman GR, Pande VS. Protein folded states are kinetic hubs. Proceedings of the National Academy of Sciences of the United States of America. 107: 10890-5. PMID 20534497 DOI: 10.1073/pnas.1003962107  1
2010 Bowman GR, Huang X, Pande VS. Network models for molecular kinetics and their initial applications to human health. Cell Research. 20: 622-30. PMID 20421891 DOI: 10.1038/cr.2010.57  1
2010 Voelz VA, Bowman GR, Beauchamp K, Pande VS. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). Journal of the American Chemical Society. 132: 1526-8. PMID 20070076 DOI: 10.1021/ja9090353  1
2010 Huang X, Yao Y, Bowman GR, Sun J, Guibas LJ, Carlsson G, Pande VS. Constructing multi-resolution markov state models (MSMS) to elucidate RNA hairpin folding mechanisms Pacific Symposium On Biocomputing 2010, Psb 2010. 228-239. PMID 19908375  1
2010 Bowman GR, Pande VS. Protein folded states are kinetic hubs (Proceedings of the National Academy of Sciences of the United States of America (2010) 107, (10890-10895) DOI: 10.1073/pnas.1003962107) Proceedings of the National Academy of Sciences of the United States of America. 107: 16749. DOI: 10.1073/pnas.1012332107  1
2009 Huang X, Bowman GR, Bacallado S, Pande VS. Rapid equilibrium sampling initiated from nonequilibrium data. Proceedings of the National Academy of Sciences of the United States of America. 106: 19765-9. PMID 19805023 DOI: 10.1073/pnas.0909088106  1
2009 Bowman GR, Beauchamp KA, Boxer G, Pande VS. Progress and challenges in the automated construction of Markov state models for full protein systems. The Journal of Chemical Physics. 131: 124101. PMID 19791846 DOI: 10.1063/1.3216567  1
2009 Bowman GR, Pande VS. The roles of entropy and kinetics in structure prediction. Plos One. 4: e5840. PMID 19513117 DOI: 10.1371/journal.pone.0005840  1
2009 Bowman GR, Huang X, Pande VS. Using generalized ensemble simulations and Markov state models to identify conformational states. Methods (San Diego, Calif.). 49: 197-201. PMID 19410002 DOI: 10.1016/j.ymeth.2009.04.013  1
2009 Voelz VA, Luttmann E, Bowman GR, Pande VS. Probing the nanosecond dynamics of a designed three-stranded beta-sheet with a massively parallel molecular dynamics simulation. International Journal of Molecular Sciences. 10: 1013-30. PMID 19399235 DOI: 10.3390/ijms10031013  1
2009 Yao Y, Sun J, Huang X, Bowman GR, Singh G, Lesnick M, Guibas LJ, Pande VS, Carlsson G. Topological methods for exploring low-density states in biomolecular folding pathways. The Journal of Chemical Physics. 130: 144115. PMID 19368437 DOI: 10.1063/1.3103496  1
2009 Bowman GR, Pande VS. Simulated tempering yields insight into the low-resolution Rosetta scoring functions. Proteins. 74: 777-88. PMID 18767152 DOI: 10.1002/prot.22210  1
2008 Bowman GR, Huang X, Yao Y, Sun J, Carlsson G, Guibas LJ, Pande VS. Structural insight into RNA hairpin folding intermediates. Journal of the American Chemical Society. 130: 9676-8. PMID 18593120 DOI: 10.1021/ja8032857  1
2008 Huang X, Bowman GR, Pande VS. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. The Journal of Chemical Physics. 128: 205106. PMID 18513049 DOI: 10.1063/1.2908251  1
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