Effect of solvent model when probing protein dynamics with molecular dynamics
Tài liệu tham khảo
Case, 2002, Acc. Chem. Res., 35, 325, 10.1021/ar010020l
Schlick, 2011, Q. Rev. Biophys., 44, 191, 10.1017/S0033583510000284
Dror, 2012, Annu. Rev. Biophys., 41, 429, 10.1146/annurev-biophys-042910-155245
Bryant, 1996, Annu. Rev. Biophys. Biomol. Struct., 25, 29, 10.1146/annurev.bb.25.060196.000333
Prabhu, 2006, Chem. Rev., 106, 1616, 10.1021/cr040437f
Tarek, 2000, J. Biophys., 79, 3244, 10.1016/S0006-3495(00)76557-X
Perez, 2009, Annu. Rep. Comput. Chem., 5, 79, 10.1016/S1574-1400(09)00504-0
Huber, 1994, J. Comput. Aided. Mol. Des., 8, 695, 10.1007/BF00124016
Hamelberg, 2004, J. Chem. Phys., 120, 11919, 10.1063/1.1755656
Barducci, 2008, Phys. Rev. Lett., 100, 020603, 10.1103/PhysRevLett.100.020603
Swendsen, 1986, Phys. Rev. Lett., 57, 2607, 10.1103/PhysRevLett.57.2607
Woods, 2003, J. Phys. Chem. B, 107, 13703, 10.1021/jp0356620
West, 2007, J. Chem. Phys., 126, 145104, 10.1063/1.2716389
Chodera, 2014, Curr. Opin. Struct. Biol., 25, 135, 10.1016/j.sbi.2014.04.002
Bond, 2007, J. Struct. Biol., 157, 593, 10.1016/j.jsb.2006.10.004
Saunders, 2013, Annu. Rev. Biophys., 42, 73, 10.1146/annurev-biophys-083012-130348
de Jong, 2013, J. Chem. Theory Comput., 9, 687, 10.1021/ct300646g
Kar, 2013, J. Chem. Theory Comput., 9, 3769, 10.1021/ct400230y
Knotts, 2007, J. Chem. Phys., 126, 084901, 10.1063/1.2431804
Linak, 2010, J. Chem. Phys., 133, 125101, 10.1063/1.3480685
Marrink, 2004, J. Phys. Chem. B, 108, 750, 10.1021/jp036508g
Orsi, 2008, J. Phys. Chem. B, 112, 802, 10.1021/jp076139e
Rusu, 2014, J. Chem. Theory Comput., 10, 5068, 10.1021/ct500455u
Riniker, 2011, J. Chem. Phys., 134, 084110, 10.1063/1.3553378
Marrink, 2007, J. Phys. Chem. B, 111, 7812, 10.1021/jp071097f
Orsi, 2011, PLoS One, 6, e28637, 10.1371/journal.pone.0028637
Riniker, 2012, J. Eur. Biophys., 41, 647, 10.1007/s00249-012-0837-1
Wassenaar, 2013, J. Phys. Chem. B, 117, 3516, 10.1021/jp311533p
Orsi, 2014, J. Chem. Theory Comput., 10, 4684, 10.1021/ct500065k
Genheden, 2016, J. Chem. Theory Comput., 12, 297, 10.1021/acs.jctc.5b00963
Chen, 2008, Curr. Opin. Struct. Biol., 18, 140, 10.1016/j.sbi.2008.01.003
Baker, 2005, Curr. Opin. Struct. Biol., 15, 137, 10.1016/j.sbi.2005.02.001
Baker, 2004, Methods Enzymol., 383, 94, 10.1016/S0076-6879(04)83005-2
Lee, 2002, J. Chem. Phys., 116, 10606, 10.1063/1.1480013
Im, 2003, J. Comput. Chem., 24, 1691, 10.1002/jcc.10321
Onufriev, 2004, Proteins, 55, 383, 10.1002/prot.20033
Haberthür, 2008, J. Comput. Chem., 29, 701, 10.1002/jcc.20832
Gallicchio, 2009, J. Chem. Theory Comput., 5, 2544, 10.1021/ct900234u
Mobley, 2008, J. Phys. Chem. B, 112, 938, 10.1021/jp0764384
Knight, 2011, J. Comput. Chem., 32, 2909, 10.1002/jcc.21876
Zhou, 2003, Proteins, 53, 148, 10.1002/prot.10483
Nymeyer, 2003, Proc. Natl. Acad. Sci. U. S. A., 100, 13934, 10.1073/pnas.2232868100
Srinivasan, 1998, J. Am. Chem. Soc., 120, 9401, 10.1021/ja981844+
Li, 2009, J. Am. Chem. Soc., 131, 7226, 10.1021/ja902477s
Anandakrishnan, 2015, J. Biophys., 108, 1153, 10.1016/j.bpj.2014.12.047
Li, 2005, Proteins, 60, 464, 10.1002/prot.20470
Tan, 2006, J. Phys. Chem. B, 110, 18680, 10.1021/jp063479b
Hua, 2016, Protein Sci., 26, 204, 10.1002/pro.2753
Akke, 1993, J. Am. Chem. Soc., 115, 9832, 10.1021/ja00074a073
Igumenova, 2006, Chem. Rev., 106, 1672, 10.1021/cr040422h
Gu, 2014, J. Chem. Theory Comput., 10, 2599, 10.1021/ct500181v
Trbovic, 2009, J. Am. Chem. Soc., 131, 615, 10.1021/ja806475k
Diehl, 2009, J. Biomol. NMR, 45, 157, 10.1007/s10858-009-9356-5
Allnér, 2015, J. Phys. Chem. B, 119, 1114, 10.1021/jp506609g
Diehl, 2010, J. Am. Chem. Soc., 132, 14577, 10.1021/ja105852y
Soares, 2004, J. Biomol. NMR, 30, 407, 10.1007/s10858-004-5430-1
Showalter, 2007, J. Chem. Theory Comput., 3, 961, 10.1021/ct7000045
Genheden, 2012, Phys. Chem. Chem. Phys., 14, 8662, 10.1039/c2cp23961b
Hornak, 2006, Proteins, 65, 712, 10.1002/prot.21123
Kirschner, 2008, J. Comput. Chem., 29, 622, 10.1002/jcc.20820
Wang, 2004, J. Comput. Chem., 25, 1157, 10.1002/jcc.20035
Horn, 2004, J. Chem. Phys., 120, 9665, 10.1063/1.1683075
Plimpton, 1995, J. Comput. Phys., 117, 1, 10.1006/jcph.1995.1039
Feenstra, 1999, J. Comput. Chem., 20, 786, 10.1002/(SICI)1096-987X(199906)20:8<786::AID-JCC5>3.0.CO;2-B
Genheden, 2015, J. Chem. Theory Comput., 11, 4749, 10.1021/acs.jctc.5b00469
Ryckaert, 1977, J. Comput. Phys., 23, 327, 10.1016/0021-9991(77)90098-5
Hockney, 1989, 26
Hünenberger, 2005, Adv. Polym. Sci., 173, 105, 10.1007/b99427
Berendsen, 1984, J. Chem. Phys., 81, 3684, 10.1063/1.448118
Salomon-Ferrer, 2013, Wiley Interdiscip. Rev. Comput. Mol. Sci., 3, 198, 10.1002/wcms.1121
Weiser, 1999, J. Comput. Chem., 20, 217, 10.1002/(SICI)1096-987X(19990130)20:2<217::AID-JCC4>3.0.CO;2-A
Prompers, 2002, J. Am. Chem. Soc., 124, 4522, 10.1021/ja012750u
Genheden, 2014, J. Chem. Theory Comput., 10, 432, 10.1021/ct400747s
Mobley, 2009, J. Chem. Theory Comput., 5, 350, 10.1021/ct800409d
Truchon, 2009, J. Chem. Inf. Model., 47, 488, 10.1021/ci600426e
Swamidass, 2010, Bioinformatics, 26, 1346, 10.1093/bioinformatics/btq140
Michaud-Agrawal, 2011, J. Comput. Chem., 32, 2319, 10.1002/jcc.21787
Hanson, 2003, J. Mol. Biol., 333, 425, 10.1016/j.jmb.2003.08.023
Gu, 2014, J. Chem. Theory Comput., 10, 2599, 10.1021/ct500181v
Lindorff-Larsen, 2012, PLoS One, 7, e32131, 10.1371/journal.pone.0032131
Vitalini, 2015, J. Chem. Phys., 142, 084101, 10.1063/1.4909549