| Year |
Citation |
Score |
| 2024 |
Smith LG, Novak B, Osato M, Mobley DL, Bowman GR. PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model. Journal of Chemical Theory and Computation. PMID 38291966 DOI: 10.1021/acs.jctc.3c00870 |
0.302 |
|
| 2023 |
Boby ML, Fearon D, Ferla M, Filep M, Koekemoer L, Robinson MC, Chodera JD, Lee AA, London N, von Delft A, von Delft F, Achdout H, Aimon A, Alonzi DS, Arbon R, ... ... Bowman GR, et al. Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors. Science (New York, N.Y.). 382: eabo7201. PMID 37943932 DOI: 10.1126/science.abo7201 |
0.745 |
|
| 2023 |
Voelz VA, Pande VS, Bowman GR. Folding@home: achievements from over twenty years of citizen science herald the exascale era. Arxiv. PMID 36994157 |
0.728 |
|
| 2023 |
Meller A, Bhakat S, Solieva S, Bowman GR. Accelerating Cryptic Pocket Discovery Using AlphaFold. Journal of Chemical Theory and Computation. PMID 36948209 DOI: 10.1021/acs.jctc.2c01189 |
0.734 |
|
| 2023 |
Voelz VA, Pande VS, Bowman GR. Folding@home: Achievements from over 20 years of citizen science herald the exascale era. Biophysical Journal. PMID 36945779 DOI: 10.1016/j.bpj.2023.03.028 |
0.727 |
|
| 2023 |
Meller A, Ward M, Borowsky J, Kshirsagar M, Lotthammer JM, Oviedo F, Ferres JL, Bowman GR. Predicting locations of cryptic pockets from single protein structures using the PocketMiner graph neural network. Nature Communications. 14: 1177. PMID 36859488 DOI: 10.1038/s41467-023-36699-3 |
0.326 |
|
| 2023 |
Stuchell-Brereton MD, Zimmerman MI, Miller JJ, Mallimadugula UL, Incicco JJ, Roy D, Smith LG, Cubuk J, Baban B, DeKoster GT, Frieden C, Bowman GR, Soranno A. Apolipoprotein E4 has extensive conformational heterogeneity in lipid-free and lipid-bound forms. Proceedings of the National Academy of Sciences of the United States of America. 120: e2215371120. PMID 36749730 DOI: 10.1073/pnas.2215371120 |
0.708 |
|
| 2023 |
Meller A, Lotthammer JM, Smith LG, Novak B, Lee LA, Kuhn CC, Greenberg L, Leinwand LA, Greenberg MJ, Bowman GR. Drug specificity and affinity are encoded in the probability of cryptic pocket opening in myosin motor domains. Elife. 12. PMID 36705568 DOI: 10.7554/eLife.83602 |
0.302 |
|
| 2023 |
Tamadonfar KO, Di Venanzio G, Pinkner JS, Dodson KW, Kalas V, Zimmerman MI, Bazan Villicana J, Bowman GR, Feldman MF, Hultgren SJ. Structure-function correlates of fibrinogen binding by adhesins critical in catheter-associated urinary tract infections. Proceedings of the National Academy of Sciences of the United States of America. 120: e2212694120. PMID 36652481 DOI: 10.1073/pnas.2212694120 |
0.68 |
|
| 2022 |
Knapp BD, Ward MD, Bowman GR, Shi H, Huang KC. Multiple conserved states characterize the twist landscape of the bacterial actin homolog MreB. Computational and Structural Biotechnology Journal. 20: 5838-5846. PMID 36382191 DOI: 10.1016/j.csbj.2022.10.008 |
0.323 |
|
| 2022 |
Polino AJ, Miller JJ, Bhakat S, Mukherjee S, Bobba S, Bowman GR, Goldberg DE. The nepenthesin insert in the Plasmodium falciparum aspartic protease plasmepsin V is necessary for enzyme function. The Journal of Biological Chemistry. 102355. PMID 35952758 DOI: 10.1016/j.jbc.2022.102355 |
0.676 |
|
| 2022 |
Cruz MA, Frederick TE, Mallimadugula UL, Singh S, Vithani N, Zimmerman MI, Porter JR, Moeder KE, Amarasinghe GK, Bowman GR. A cryptic pocket in Ebola VP35 allosterically controls RNA binding. Nature Communications. 13: 2269. PMID 35477718 DOI: 10.1038/s41467-022-29927-9 |
0.746 |
|
| 2021 |
Knoverek CR, Mallimadugula UL, Singh S, Rennella E, Frederick TE, Yuwen T, Raavicharla S, Kay LE, Bowman GR. Opening of a cryptic pocket in β-lactamase increases penicillinase activity. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34799442 DOI: 10.1073/pnas.2106473118 |
0.475 |
|
| 2021 |
Malik M, Ward MD, Fang Y, Porter JR, Zimmerman MI, Koelblen T, Roh M, Frolova AI, Burris TP, Bowman GR, Imoukhuede PI, England SK. Naturally Occurring Genetic Variants in the Oxytocin Receptor Alter Receptor Signaling Profiles. Acs Pharmacology & Translational Science. 4: 1543-1555. PMID 34661073 DOI: 10.1021/acsptsci.1c00095 |
0.664 |
|
| 2021 |
Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, ... ... Bowman GR, et al. SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome. Nature Chemistry. PMID 34031561 DOI: 10.1038/s41557-021-00707-0 |
0.813 |
|
| 2021 |
Ward MD, Zimmerman MI, Meller A, Chung M, Swamidass SJ, Bowman GR. Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets. Nature Communications. 12: 3023. PMID 34021153 DOI: 10.1038/s41467-021-23246-1 |
0.722 |
|
| 2021 |
Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR. SARS-CoV2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biophysical Journal. PMID 33794150 DOI: 10.1016/j.bpj.2021.03.024 |
0.76 |
|
| 2021 |
Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nature Communications. 12: 1936. PMID 33782395 DOI: 10.1038/s41467-021-21953-3 |
0.729 |
|
| 2020 |
Vithani N, Ward MD, Zimmerman MI, Novak B, Borowsky JH, Singh S, Bowman GR. SARS-CoV-2 Nsp16 activation mechanism and a cryptic pocket with pan-coronavirus antiviral potential. Biorxiv : the Preprint Server For Biology. PMID 33330873 DOI: 10.1101/2020.12.10.420109 |
0.76 |
|
| 2020 |
Riehl JR, Zimmerman MI, Singh MF, Bowman GR, Ching S. Computing and optimizing over all fixed-points of discrete systems on large networks. Journal of the Royal Society, Interface. 17: 20200126. PMID 32900299 DOI: 10.1098/Rsif.2020.0126 |
0.693 |
|
| 2020 |
Zimmerman MI, Porter JR, Ward MD, Singh S, Vithani N, Meller A, Mallimadugula UL, Kuhn CE, Borowsky JH, Wiewiora RP, Hurley MFD, Harbison AM, Fogarty CA, Coffland JE, Fadda E, ... ... Bowman GR, et al. Citizen Scientists Create an Exascale Computer to Combat COVID-19. Biorxiv : the Preprint Server For Biology. PMID 32637963 DOI: 10.1101/2020.06.27.175430 |
0.81 |
|
| 2020 |
Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Biorxiv : the Preprint Server For Biology. PMID 32587966 DOI: 10.1101/2020.06.17.158121 |
0.733 |
|
| 2020 |
Porter JR, Meller A, Zimmerman MI, Greenberg MJ, Bowman GR. Conformational distributions of isolated myosin motor domains encode their mechanochemical properties. Elife. 9. PMID 32479265 DOI: 10.7554/Elife.55132 |
0.71 |
|
| 2020 |
Brown CA, Hu L, Sun Z, Patel MP, Singh S, Porter JR, Sankaran B, Prasad BVV, Bowman GR, Palzkill T. Antagonism between substitutions in β-lactamase explains a path not taken in the evolution of bacterial drug resistance. The Journal of Biological Chemistry. PMID 32299911 DOI: 10.1074/Jbc.Ra119.012489 |
0.442 |
|
| 2020 |
Brown CA, Hu L, Sun Z, Patel MP, Singh S, Porter JR, Sankaran B, Prasad BVV, Bowman GR, Palzkill T. Antagonism between substitutions in β-lactamase explains a path not taken in the evolution of bacterial drug resistance. The Journal of Biological Chemistry. PMID 32299911 DOI: 10.1074/Jbc.Ra119.012489 |
0.442 |
|
| 2020 |
Kuzmanic A, Bowman GR, Juarez-Jimenez J, Michel J, Gervasio FL. Investigating Cryptic Binding Sites by Molecular Dynamics Simulations. Accounts of Chemical Research. PMID 32134250 DOI: 10.1021/Acs.Accounts.9B00613 |
0.349 |
|
| 2020 |
Behring JB, van der Post S, Mooradian AD, Egan MJ, Zimmerman MI, Clements JL, Bowman GR, Held JM. Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation. Science Signaling. 13. PMID 31964804 DOI: 10.1126/Scisignal.Aay7315 |
0.707 |
|
| 2020 |
Wang W, Shin WJ, Zhang B, Choi Y, Yoo JS, Zimmerman MI, Frederick TE, Bowman GR, Gross ML, Leung DW, Jung JU, Amarasinghe GK. The Cap-Snatching SFTSV Endonuclease Domain Is an Antiviral Target. Cell Reports. 30: 153-163.e5. PMID 31914382 DOI: 10.1016/J.Celrep.2019.12.020 |
0.687 |
|
| 2020 |
Porter JR, Meller A, Zimmerman MI, Greenberg MJ, Bowman GR. Author response: Conformational distributions of isolated myosin motor domains encode their mechanochemical properties Elife. DOI: 10.7554/Elife.55132.Sa2 |
0.675 |
|
| 2020 |
Porter JR, Meller A, Zimmerman MI, Greenberg MJ, Bowman G. Myosin Motors’ Kinetic Diversity is Encoded by the Conformational Dynamics of the Motor Domain Biophysical Journal. 118: 434a. DOI: 10.1016/J.Bpj.2019.11.2436 |
0.694 |
|
| 2020 |
Zimmerman MI, Bowman G. Fast Conformational Searches to Characterize the Effects of Mutations on Complex Landscapes Biophysical Journal. 118: 205a-206a. DOI: 10.1016/J.Bpj.2019.11.1234 |
0.683 |
|
| 2019 |
Porter JR, Moeder KE, Sibbald CA, Zimmerman MI, Hart KM, Greenberg MJ, Bowman GR. Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling. Biophysical Journal. PMID 30744991 DOI: 10.1016/J.Bpj.2018.11.3144 |
0.743 |
|
| 2019 |
Porter JR, Zimmerman MI, Bowman GR. Enspara: Modeling molecular ensembles with scalable data structures and parallel computing. The Journal of Chemical Physics. 150: 044108. PMID 30709308 DOI: 10.1063/1.5063794 |
0.745 |
|
| 2019 |
Bowman GR, Lindahl E. Decision letter: The dynamic conformational landscape of the protein methyltransferase SETD8 Elife. DOI: 10.7554/Elife.45403.074 |
0.348 |
|
| 2019 |
Porter JR, Moeder KE, Sibbald CA, Zimmerman MI, Hart KM, Greenberg MJ, Bowman GR. Cooperative changes in solvent exposure identify cryptic pockets, conformational switches and allosteric coupling Acta Crystallographica Section a Foundations and Advances. 75: a432-a432. DOI: 10.1107/S0108767319095795 |
0.682 |
|
| 2018 |
Knoverek CR, Amarasinghe GK, Bowman GR. Advanced Methods for Accessing Protein Shape-Shifting Present New Therapeutic Opportunities. Trends in Biochemical Sciences. PMID 30555007 DOI: 10.1016/J.Tibs.2018.11.007 |
0.424 |
|
| 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 |
0.553 |
|
| 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 |
0.749 |
|
| 2018 |
Sun X, Singh S, Blumer KJ, Bowman GR. Author response: Simulation of spontaneous G protein activation reveals a new intermediate driving GDP unbinding Elife. DOI: 10.7554/Elife.38465.031 |
0.521 |
|
| 2018 |
Frederick TE, Hart KM, Moeder KE, Ho CM, Zimmerman MI, Bowman GR. Boltzmann Docking Identifies Allosteric Small Molecule Modulators of Protein Activity Biophysical Journal. 114: 58a. DOI: 10.1016/J.Bpj.2017.11.369 |
0.707 |
|
| 2018 |
Singh S, Sun X, Blumer KJ, Bowman GR. Direct Observation of GDP Unbinding Reveals Multiple Allosteric Pathways Underlie G-Protein Activation Biophysical Journal. 114: 398a. DOI: 10.1016/J.Bpj.2017.11.2202 |
0.483 |
|
| 2017 |
Zimmerman MI, Hart KM, Sibbald CA, Frederick TE, Jimah JR, Knoverek CR, Tolia NH, Bowman GR. Prediction of New Stabilizing Mutations Based on Mechanistic Insights from Markov State Models. Acs Central Science. 3: 1311-1321. PMID 29296672 DOI: 10.1016/J.Bpj.2017.11.2283 |
0.732 |
|
| 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 |
0.439 |
|
| 2017 |
Hart KM, Moeder KE, Ho CMW, Zimmerman MI, Frederick TE, Bowman GR. Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators. Plos One. 12: e0178678. PMID 28570708 DOI: 10.1371/Journal.Pone.0178678 |
0.72 |
|
| 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 |
0.511 |
|
| 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 |
0.325 |
|
| 2017 |
Tainer JA, Shen R, Ho C, Long WZ, Singh S, Burnett K, Hura GL, Nix JC, Bowman GR, Ellenberger T, Brosey CA. Defining allostery and interactions regulating apoptosis-inducing factor Acta Crystallographica Section a Foundations and Advances. 73: a316-a316. DOI: 10.1107/S0108767317096908 |
0.386 |
|
| 2017 |
Singh S, Bowman GR. Quantifying Allosteric Communication via Correlations in Structure and Disorder Biophysical Journal. 112: 498a. DOI: 10.1016/J.Bpj.2016.11.2693 |
0.416 |
|
| 2017 |
Zimmerman MI, Bowman GR. Fast Forward Protein Folding Biophysical Journal. 112: 323a. DOI: 10.1016/J.Bpj.2016.11.1750 |
0.765 |
|
| 2016 |
Shen G, Cui W, Zhang H, Zhou F, Huang W, Liu Q, Yang Y, Li S, Bowman GR, Sadler JE, Gross ML, Li W. Warfarin traps human vitamin K epoxide reductase in an intermediate state during electron transfer. Nature Structural & Molecular Biology. PMID 27918545 DOI: 10.1038/Nsmb.3333 |
0.377 |
|
| 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 |
0.486 |
|
| 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 |
0.397 |
|
| 2016 |
Zimmerman MI, Bowman GR. How to Run FAST Simulations. Methods in Enzymology. 578: 213-25. PMID 27497168 DOI: 10.1016/Bs.Mie.2016.05.032 |
0.757 |
|
| 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 |
0.754 |
|
| 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 |
0.772 |
|
| 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 |
0.394 |
|
| 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 |
0.365 |
|
| 2015 |
DuBay KH, Bowman GR, Geissler PL. Fluctuations within folded proteins: implications for thermodynamic and allosteric regulation. Accounts of Chemical Research. 48: 1098-105. PMID 25688669 DOI: 10.1021/Ar500351B |
0.447 |
|
| 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 |
0.483 |
|
| 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 |
0.801 |
|
| 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 |
0.358 |
|
| 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 |
0.404 |
|
| 2014 |
Bolin E, Maguire B, Bowman G, Marqusee S. Thiol Labeling Reveals Presence of Cryptic Binding Sites in β-Lactamase Biophysical Journal. 106: 658a. DOI: 10.1016/J.Bpj.2013.11.3642 |
0.373 |
|
| 2014 |
Bowman GR, Geissler PL, Marqusee S. Finding Hidden Allosteric Sites in Proteins Biophysical Journal. 106: 647a. DOI: 10.1016/J.Bpj.2013.11.3581 |
0.379 |
|
| 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 |
0.488 |
|
| 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 |
0.542 |
|
| 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 |
0.533 |
|
| 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 |
0.425 |
|
| 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 |
0.367 |
|
| 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 |
0.416 |
|
| 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 |
0.759 |
|
| 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 |
0.444 |
|
| 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 |
0.536 |
|
| 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 |
0.759 |
|
| 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 |
0.743 |
|
| 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 |
0.55 |
|
| 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 |
0.748 |
|
| 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 |
0.728 |
|
| 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 |
0.647 |
|
| 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 |
0.469 |
|
| 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 |
0.582 |
|
| 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 |
0.583 |
|
| 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 |
0.602 |
|
| 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 |
0.635 |
|
| 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 |
0.76 |
|
| 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 |
0.609 |
|
| 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 |
0.461 |
|
| 2010 |
Bowman GR, Pande VS. Millisecond Timescale, Atomistic Protein Folding Simulations Yield a Network Theory for Protein Folding Biophysical Journal. 98: 614a. DOI: 10.1016/J.Bpj.2009.12.3352 |
0.622 |
|
| 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 |
0.638 |
|
| 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 |
0.604 |
|
| 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 |
0.563 |
|
| 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 |
0.653 |
|
| 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 |
0.716 |
|
| 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 |
0.651 |
|
| 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 |
0.568 |
|
| 2009 |
Bowman GR, Huang X, Pande VS. Adaptive Seeding: A New Method for Simulating Biologically Relevant Timescales Biophysical Journal. 96: 575a. DOI: 10.1016/J.Bpj.2008.12.3002 |
0.673 |
|
| 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 |
0.659 |
|
| 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 |
0.616 |
|
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