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Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units

dc.contributor.authorGong, Xiping
dc.contributor.authorChiricotto, Mara
dc.contributor.authorLiu, Xiaorong
dc.contributor.authorNordquist, Erik
dc.contributor.authorFeig, Michael
dc.contributor.authorBrooks, Charles L.
dc.contributor.authorChen, Jianhan
dc.date.accessioned2020-03-17T18:34:11Z
dc.date.availableWITHHELD_13_MONTHS
dc.date.available2020-03-17T18:34:11Z
dc.date.issued2020-03-30
dc.identifier.citationGong, Xiping; Chiricotto, Mara; Liu, Xiaorong; Nordquist, Erik; Feig, Michael; Brooks, Charles L.; Chen, Jianhan (2020). "Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units." Journal of Computational Chemistry 41(8): 830-838.
dc.identifier.issn0192-8651
dc.identifier.issn1096-987X
dc.identifier.urihttps://hdl.handle.net/2027.42/154497
dc.publisherJohn Wiley & Sons, Inc.
dc.subject.otherprotein conformation
dc.subject.otherOpenMM
dc.subject.othergeneralized Born
dc.subject.otherCHARMM
dc.subject.othersolvation free energy
dc.titleAccelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units
dc.typeArticle
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelChemistry
dc.subject.hlbsecondlevelMaterials Science and Engineering
dc.subject.hlbsecondlevelChemical Engineering
dc.subject.hlbtoplevelEngineering
dc.subject.hlbtoplevelScience
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/154497/1/jcc26133.pdf
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/154497/2/jcc26133_am.pdf
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/154497/3/jcc26133-sup-0001-supinfo.pdf
dc.identifier.doi10.1002/jcc.26133
dc.identifier.sourceJournal of Computational Chemistry
dc.identifier.citedreferenceB. Hess, C. Kutzner, D. van der Spoel, E. Lindahl, J. Chem. Theory Comput. 2008, 4, 435.
dc.identifier.citedreferenceJ. H. Chen, J. Chem. Theory Comput. 2010, 6, 2790.
dc.identifier.citedreferenceA. Ghosh, C. S. Rapp, R. A. Friesner, J. Phys. Chem. B 1998, 102, 10983.
dc.identifier.citedreferenceM. S. Lee, F. R. Salsbury, C. L. Brooks, J. Chem. Phys. 2002, 116, 10606.
dc.identifier.citedreferenceM. S. Lee, M. Feig, F. R. Salsbury, C. L. Brooks, J. Comput. Chem. 2003, 24, 1348.
dc.identifier.citedreferenceJ. Chocholousova, M. Feig, J. Comput. Chem. 2006, 27, 719.
dc.identifier.citedreferenceJ. Mongan, C. Simmerling, J. A. McCammon, D. A. Case, A. Onufriev, J. Chem. Theory Comput. 2007, 3, 156.
dc.identifier.citedreferenceH. Nguyen, D. R. Roe, C. Simmerling, J. Chem. Theory Comput. 2013, 9, 2020.
dc.identifier.citedreferenceK. H. Lee, J. H. Chen, J. Comput. Chem. 2017, 38, 1332.
dc.identifier.citedreferenceF. M. Richards, Annu. Rev. Biophys. Biol. 1977, 6, 151.
dc.identifier.citedreferenceA. Juneja, M. Ito, L. Nilsson, J. Chem. Theory Comput. 2013, 9, 834.
dc.identifier.citedreferenceJ. L. Knight, C. L. Brooks, J. Comput. Chem. 2011, 32, 2909.
dc.identifier.citedreferenceX. R. Liu, J. H. Chen, J. Chem. Theory Comput. 2019, 15, 4708.
dc.identifier.citedreferenceR. B. Best, W. W. Zheng, J. Mittal, J. Chem. Theory Comput. 2014, 10, 5113.
dc.identifier.citedreferenceS. Piana, J. L. Klepeis, D. E. Shaw, Curr. Opin. Struc. Biol. 2014, 24, 98.
dc.identifier.citedreferenceS. Piana, A. G. Donchev, P. Robustelli, D. E. Shaw, J. Phys. Chem. B 2015, 119, 5113.
dc.identifier.citedreferenceB. R. Brooks, C. L. Brooks, A. D. Mackerell, L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus, J. Comput. Chem. 2009, 30, 1545.
dc.identifier.citedreferenceD. A. Case, T. E. Cheatham, T. Darden, H. Gohlke, R. Luo, K. M. Merz, A. Onufriev, C. Simmerling, B. Wang, R. J. Woods, J. Comput. Chem. 2005, 26, 1668.
dc.identifier.citedreferenceR. Salomon‐Ferrer, A. W. Gotz, D. Poole, S. Le Grand, R. C. Walker, J. Chem. Theory Comput. 2013, 9, 3878.
dc.identifier.citedreferenceJ. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, K. Schulten, J. Comput. Chem. 2005, 26, 1781.
dc.identifier.citedreferenceD. E. Tanner, J. C. Phillips, K. Schulten, J. Chem. Theory Comput. 2012, 8, 2521.
dc.identifier.citedreferenceP. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane, L. P. Wang, D. Shukla, T. Tye, M. Houston, T. Stich, C. Klein, M. R. Shirts, V. S. Pande, J. Chem. Theory Comput. 2013, 9, 461.
dc.identifier.citedreferenceA. W. Gotz, M. J. Williamson, D. Xu, D. Poole, S. Le Grand, R. C. Walker, J. Chem. Theory Comput. 2012, 8, 1542.
dc.identifier.citedreferenceE. J. Arthur, C. L. Brooks, J. Comput. Chem. 2016, 37, 927.
dc.identifier.citedreferenceH. Huang, C. Simmerling, J. Chem. Theory Comput. 2018, 14, 5797.
dc.identifier.citedreferenceR. M. Levy, L. Y. Zhang, E. Gallicchio, A. K. Felts, J. Am. Chem. Soc. 2003, 125, 9523.
dc.identifier.citedreferenceJ. H. Chen, C. L. Brooks, J. Am. Chem. Soc. 2007, 129, 2444.
dc.identifier.citedreferenceW. C. Still, A. Tempczyk, R. C. Hawley, T. Hendrickson, J. Am. Chem. Soc. 1990, 112, 6127.
dc.identifier.citedreferenceJ. Srinivasan, M. W. Trevathan, P. Beroza, D. A. Case, Theor. Chem. Acc. 1999, 101, 426.
dc.identifier.citedreferenceS. M. Vaiana, M. Manno, A. Emanuele, M. B. Palma‐Vittorelli, M. U. Palma, J Biol Phys 2001, 27, 133.
dc.identifier.citedreferenceJ. W. Ponder, D. A. Case, Adv. Protein Chem. 2003, 66, 27.
dc.identifier.citedreferenceA. D. Mackerell, J. Comput. Chem. 2004, 25, 1584.
dc.identifier.citedreferenceJ. Wagoner, N. A. Baker, J. Comput. Chem. 2004, 25, 1623.
dc.identifier.citedreferenceA. Onufriev, D. A. Case, D. Bashford, J. Comput. Chem. 2002, 23, 1297.
dc.identifier.citedreferenceC. J. Cramer, D. G. Truhlar, Chem. Rev. 1999, 99, 2161.
dc.identifier.citedreferenceB. Roux, T. Simonson, Biophys. Chem. 1999, 78, 1.
dc.identifier.citedreferenceM. Feig, C. L. Brooks, Curr. Opin. Struct. Biol. 2004, 14, 217.
dc.identifier.citedreferenceJ. Chen, C. L. Brooks, Phys. Chem. Chem. Phys. 2008, 10, 471.
dc.identifier.citedreferenceJ. H. Chen, C. L. Brooks, J. Khandogin, Curr. Opin. Struc. Biol. 2008, 18, 140.
dc.identifier.citedreferenceN. A. Baker, Curr. Opin. Struct. Biol. 2005, 15, 137.
dc.identifier.citedreferenceM. K. Gilson, M. E. Davis, B. A. Luty, J. A. Mccammon, J. Phys. Chem. 1993, 97, 3591.
dc.identifier.citedreferenceA. Nicholls, B. Honig, J. Comput. Chem. 1991, 12, 435.
dc.identifier.citedreferenceD. Bashford, D. A. Case, Annu. Rev. Phys. Chem. 2000, 51, 129.
dc.identifier.citedreferenceV. Tsui, D. A. Case, Biopolymers 2001, 56, 275.
dc.identifier.citedreferenceU. Haberthur, A. Caflisch, J. Comput. Chem. 2008, 29, 701.
dc.identifier.citedreferenceA. Onufriev, D. Bashford, D. A. Case, Proteins 2004, 55, 383.
dc.identifier.citedreferenceE. Gallicchio, K. Paris, R. M. Levy, J. Chem. Theory Comput. 2009, 5, 2544.
dc.identifier.citedreferenceW. P. Im, M. S. Lee, C. L. Brooks, J. Comput. Chem. 2003, 24, 1691.
dc.identifier.citedreferenceJ. H. Chen, W. P. Im, C. L. Brooks, J. Am. Chem. Soc. 2006, 128, 3728.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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