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Volumn 20, Issue 11, 2014, Pages 1-14

A consistent force field parameter set for zwitterionic amino acid residues

Author keywords

AMBER; Force field; Parameterization; RESP; Zwitterionic amino acid

Indexed keywords

ACETIC ACID DERIVATIVE; ALANINE; AMINO ACID; AMMONIA; AMPHOLYTE; ARGININE; GLUTAMIC ACID; GLYCINE; HISTIDINE; HYDROGEN; LEUCINE; LIGAND; PHENYLALANINE; PROTEIN BINDING; WATER;

EID: 84912115740     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-014-2478-z     Document Type: Article
Times cited : (38)

References (61)
  • 2
    • 72449164409 scopus 로고    scopus 로고
    • Transport mechanism of a bacterial homologue of glutamate transporters
    • COI: 1:CAS:528:DC%2BD1MXhsVentLnE
    • Reyes N, Ginter C, Boudker O (2009) Transport mechanism of a bacterial homologue of glutamate transporters. Nature 462(7275):880–885. doi:10.1038/nature08616
    • (2009) Nature , vol.462 , Issue.7275 , pp. 880-885
    • Reyes, N.1    Ginter, C.2    Boudker, O.3
  • 3
    • 49249119063 scopus 로고    scopus 로고
    • Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector l-glutamine: implications of effector binding in molecular association and DNA binding
    • COI: 1:CAS:528:DC%2BD1cXpslWntr0%3D
    • Kumarevel T, Nakano N, Ponnuraj K, Gopinath SC, Sakamoto K, Shinkai A, Kumar PK, Yokoyama S (2008) Crystal structure of glutamine receptor protein from Sulfolobus tokodaii strain 7 in complex with its effector l-glutamine: implications of effector binding in molecular association and DNA binding. Nucleic Acids Res 36(14):4808–4820. doi:10.1093/nar/gkn456
    • (2008) Nucleic Acids Res , vol.36 , Issue.14 , pp. 4808-4820
    • Kumarevel, T.1    Nakano, N.2    Ponnuraj, K.3    Gopinath, S.C.4    Sakamoto, K.5    Shinkai, A.6    Kumar, P.K.7    Yokoyama, S.8
  • 4
    • 84864285157 scopus 로고    scopus 로고
    • Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria
    • COI: 1:CAS:528:DC%2BC38Xos12gs7s%3D
    • Adler-Abramovich L, Vaks L, Carny O, Trudler D, Magno A, Caflisch A, Frenkel D, Gazit E (2012) Phenylalanine assembly into toxic fibrils suggests amyloid etiology in phenylketonuria. Nat Chem Biol 8(8):701–706. doi:10.1038/nchembio.1002
    • (2012) Nat Chem Biol , vol.8 , Issue.8 , pp. 701-706
    • Adler-Abramovich, L.1    Vaks, L.2    Carny, O.3    Trudler, D.4    Magno, A.5    Caflisch, A.6    Frenkel, D.7    Gazit, E.8
  • 5
    • 38149087413 scopus 로고    scopus 로고
    • Conformational analysis of l-prolines in water
    • COI: 1:CAS:528:DC%2BD2sXhtlaktbbE
    • Aliev AE, Courtier-Murias D (2007) Conformational analysis of l-prolines in water. J Phys Chem B 111(50):14034–14042. doi:10.1021/jp076729c
    • (2007) J Phys Chem B , vol.111 , Issue.50 , pp. 14034-14042
    • Aliev, A.E.1    Courtier-Murias, D.2
  • 6
    • 84885436030 scopus 로고    scopus 로고
    • Molecular dynamics study of the influence of solvents on the chiral discrimination of alanine enantiomers by beta-cyclodextrin
    • COI: 1:CAS:528:DC%2BC3sXhs1Wjsr7F
    • Alvira E (2013) Molecular dynamics study of the influence of solvents on the chiral discrimination of alanine enantiomers by beta-cyclodextrin. Tetrahedron Asymmetry 24:1198–1206. doi:10.1016/j.tetasy.2013.08.006
    • (2013) Tetrahedron Asymmetry , vol.24 , pp. 1198-1206
    • Alvira, E.1
  • 7
    • 84885405882 scopus 로고    scopus 로고
    • Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other
    • Andrews CT, Elcock AH (2013) Molecular dynamics simulations of highly crowded amino acid solutions: comparisons of eight different force field combinations with experiment and with each other. J Chem Theory Comput 9 (10). doi:10.1021/ct400371h
    • (2013) J Chem Theory Comput , vol.9 , Issue.10
    • Andrews, C.T.1    Elcock, A.H.2
  • 8
    • 33748994553 scopus 로고    scopus 로고
    • Molecular dynamics simulation of glycine zwitterion in aqueous solution
    • Campo MG (2006) Molecular dynamics simulation of glycine zwitterion in aqueous solution. J Chem Phys 125(11):114511. doi:10.1063/1.2352756
    • (2006) J Chem Phys , vol.125 , Issue.11 , pp. 114511
    • Campo, M.G.1
  • 9
    • 0001116890 scopus 로고
    • Molecular dynamics simulations of the conformational dynamics of tryptophan
    • COI: 1:CAS:528:DyaK38Xkt1OjtLs%3D
    • Gordon HL, Jarrell HC, Szabo AG, Willis KJ, Somorjai RL (1992) Molecular dynamics simulations of the conformational dynamics of tryptophan. J Phys Chem 96(4):1915–1921. doi:10.1021/j100183a072
    • (1992) J Phys Chem , vol.96 , Issue.4 , pp. 1915-1921
    • Gordon, H.L.1    Jarrell, H.C.2    Szabo, A.G.3    Willis, K.J.4    Somorjai, R.L.5
  • 10
    • 84860287092 scopus 로고    scopus 로고
    • Vibrational optical activity of cysteine in aqueous solution: a comparison of theoretical and experimental spectra
    • COI: 1:CAS:528:DC%2BC38Xks1Cju78%3D
    • Kaminski M, Kudelski A, Pecul M (2012) Vibrational optical activity of cysteine in aqueous solution: a comparison of theoretical and experimental spectra. J Phys Chem B 116(16):4976–4990. doi:10.1021/jp300699e
    • (2012) J Phys Chem B , vol.116 , Issue.16 , pp. 4976-4990
    • Kaminski, M.1    Kudelski, A.2    Pecul, M.3
  • 11
    • 0036776358 scopus 로고    scopus 로고
    • Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations
    • COI: 1:CAS:528:DC%2BD38XmsVKgsL4%3D
    • Mark P, Nilsson L (2002) Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations. J Comput Chem 23(13):1211–1219. doi:10.1002/jcc.10117
    • (2002) J Comput Chem , vol.23 , Issue.13 , pp. 1211-1219
    • Mark, P.1    Nilsson, L.2
  • 12
    • 58149311441 scopus 로고    scopus 로고
    • Molecular mechanism of substrate specificity in the bacterial neutral amino acid transporter LeuT
    • COI: 1:CAS:528:DC%2BD1cXhsVCls7jJ
    • Noskov SY (2008) Molecular mechanism of substrate specificity in the bacterial neutral amino acid transporter LeuT. Proteins 73(4):851–863. doi:10.1002/prot.22108
    • (2008) Proteins , vol.73 , Issue.4 , pp. 851-863
    • Noskov, S.Y.1
  • 13
    • 84879469871 scopus 로고    scopus 로고
    • Molecular basis of ligand recognition by OASS from E. histolytica: insights from structural and molecular dynamics simulation studies
    • COI: 1:CAS:528:DC%2BC3sXht1emsbjN
    • Raj I, Mazumder M, Gourinath S (2013) Molecular basis of ligand recognition by OASS from E. histolytica: insights from structural and molecular dynamics simulation studies. Biochim Biophys Acta 1830(10):4573–4583. doi:10.1016/j.bbagen.2013.05.041
    • (2013) Biochim Biophys Acta , vol.1830 , Issue.10 , pp. 4573-4583
    • Raj, I.1    Mazumder, M.2    Gourinath, S.3
  • 14
    • 84877702735 scopus 로고    scopus 로고
    • Mechanism and energetics of ligand release in the aspartate transporter GltPh
    • COI: 1:CAS:528:DC%2BC3sXmtVymtbk%3D
    • Heinzelmann G, Bastug T, Kuyucak S (2013) Mechanism and energetics of ligand release in the aspartate transporter GltPh. J Phys Chem B 117(18):5486–5496. doi:10.1021/jp4010423
    • (2013) J Phys Chem B , vol.117 , Issue.18 , pp. 5486-5496
    • Heinzelmann, G.1    Bastug, T.2    Kuyucak, S.3
  • 15
    • 84879576539 scopus 로고    scopus 로고
    • Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations
    • COI: 1:CAS:528:DC%2BC3sXntFWgtrY%3D
    • Lakkaraju SK, Xue F, Faden AI, MacKerell AD Jr (2013) Estimation of ligand efficacies of metabotropic glutamate receptors from conformational forces obtained from molecular dynamics simulations. J Chem Inf Model 53(6):1337–1349. doi:10.1021/ci400160x
    • (2013) J Chem Inf Model , vol.53 , Issue.6 , pp. 1337-1349
    • Lakkaraju, S.K.1    Xue, F.2    Faden, A.I.3    MacKerell, A.D.4
  • 16
    • 79958772218 scopus 로고    scopus 로고
    • Conformational dynamics of l-lysine, l-arginine, l-ornithine binding protein reveals ligand-dependent plasticity
    • COI: 1:CAS:528:DC%2BC3MXnt1Klt74%3D
    • Silva DA, Dominguez-Ramirez L, Rojo-Dominguez A, Sosa-Peinado A (2011) Conformational dynamics of l-lysine, l-arginine, l-ornithine binding protein reveals ligand-dependent plasticity. Proteins 79(7):2097–2108. doi:10.1002/prot.23030
    • (2011) Proteins , vol.79 , Issue.7 , pp. 2097-2108
    • Silva, D.A.1    Dominguez-Ramirez, L.2    Rojo-Dominguez, A.3    Sosa-Peinado, A.4
  • 17
    • 41449093586 scopus 로고    scopus 로고
    • Substrate binding and formation of an occluded state in the leucine transporter
    • COI: 1:CAS:528:DC%2BD1cXit1yqtLw%3D
    • Celik L, Schiott B, Tajkhorshid E (2008) Substrate binding and formation of an occluded state in the leucine transporter. Biophys J 94(5):1600–1612. doi:10.1529/biophysj.107.117580
    • (2008) Biophys J , vol.94 , Issue.5 , pp. 1600-1612
    • Celik, L.1    Schiott, B.2    Tajkhorshid, E.3
  • 18
    • 55349114344 scopus 로고    scopus 로고
    • Comparative structural dynamics of tyrosyl-tRNA synthetase complexed with different substrates explored by molecular dynamics
    • COI: 1:CAS:528:DC%2BD1cXhtlShur%2FF
    • Li T, Froeyen M, Herdewijn P (2008) Comparative structural dynamics of tyrosyl-tRNA synthetase complexed with different substrates explored by molecular dynamics. Eur Biophys J 38(1):25–35. doi:10.1007/s00249-008-0350-8
    • (2008) Eur Biophys J , vol.38 , Issue.1 , pp. 25-35
    • Li, T.1    Froeyen, M.2    Herdewijn, P.3
  • 19
    • 72249085220 scopus 로고    scopus 로고
    • Collective dynamics of periplasmic glutamine binding protein upon domain closure
    • COI: 1:CAS:528:DC%2BD1MXhsVCjtr%2FK
    • Loeffler HH, Kitao A (2009) Collective dynamics of periplasmic glutamine binding protein upon domain closure. Biophys J 97(9):2541–2549. doi:10.1016/j.bpj.2009.08.019
    • (2009) Biophys J , vol.97 , Issue.9 , pp. 2541-2549
    • Loeffler, H.H.1    Kitao, A.2
  • 21
    • 0032922174 scopus 로고    scopus 로고
    • A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat
    • COI: 1:CAS:528:DyaK1MXitF2jsb8%3D
    • Cheatham TE, Cieplak P, Kollman PA (1999) A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat. J Biomol Struct Dyn 16(4):845–862
    • (1999) J Biomol Struct Dyn , vol.16 , Issue.4 , pp. 845-862
    • Cheatham, T.E.1    Cieplak, P.2    Kollman, P.A.3
  • 22
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple amber force fields and development of improved protein backbone parameters
    • COI: 1:CAS:528:DC%2BD28XhtFWqt7fM
    • Hornak V, Abel R, Okur A, Strockbine B, Roitberg A, Simmerling C (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 65(3):712–725. doi:10.1002/Prot.21123
    • (2006) Proteins , vol.65 , Issue.3 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 23
    • 70349087354 scopus 로고    scopus 로고
    • Polarization effects in molecular mechanical force fields
    • Cieplak P, Dupradeau FY, Duan Y, Wang J (2009) Polarization effects in molecular mechanical force fields. J Phys Condens Matter 21(33):333102. doi:10.1088/0953-8984/21/33/333102
    • (2009) J Phys Condens Matter , vol.21 , Issue.33 , pp. 333102
    • Cieplak, P.1    Dupradeau, F.Y.2    Duan, Y.3    Wang, J.4
  • 24
    • 33645716062 scopus 로고    scopus 로고
    • Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides
    • COI: 1:CAS:528:DC%2BD28XjsVWnsrg%3D
    • Wang ZX, Zhang W, Wu C, Lei H, Cieplak P, Duan Y (2006) Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J Comput Chem 27(6):781–790. doi:10.1002/jcc.20386
    • (2006) J Comput Chem , vol.27 , Issue.6 , pp. 781-790
    • Wang, Z.X.1    Zhang, W.2    Wu, C.3    Lei, H.4    Cieplak, P.5    Duan, Y.6
  • 25
    • 0036890275 scopus 로고    scopus 로고
    • Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations
    • COI: 1:CAS:528:DC%2BD38XosF2rtr4%3D
    • Ren P, Ponder JW (2002) Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations. J Comput Chem 23(16):1497–1506. doi:10.1002/jcc.10127
    • (2002) J Comput Chem , vol.23 , Issue.16 , pp. 1497-1506
    • Ren, P.1    Ponder, J.W.2
  • 26
    • 23844481506 scopus 로고    scopus 로고
    • Multipole electrostatic model for MNDO-like techniques with minimal valence spd-basis sets
    • Horn AHC, Lin J-H, Clark T (114) Multipole electrostatic model for MNDO-like techniques with minimal valence spd-basis sets. Theor Chem Accounts 114(1–3):159–168. doi:10.1007/s00214-005-0657-9
    • Theor Chem Accounts , vol.114 , Issue.1-3 , pp. 159-168
    • Horn, A.H.C.1    Lin, J.-H.2    Clark, T.3
  • 27
    • 33847652241 scopus 로고    scopus 로고
    • Multipole electrostatic model for MNDO-like techniques with minimal valence spd-basis sets
    • COI: 1:CAS:528:DC%2BD2sXitlGjsrk%3D
    • Horn AHC, Lin J-H, Clark T (2007) Multipole electrostatic model for MNDO-like techniques with minimal valence spd-basis sets. Theor Chem Accounts 117(3):461–465. doi:10.1007/s00214-006-0167-4
    • (2007) Theor Chem Accounts , vol.117 , Issue.3 , pp. 461-465
    • Horn, A.H.C.1    Lin, J.-H.2    Clark, T.3
  • 28
    • 84896518999 scopus 로고    scopus 로고
    • Deriving static atomic multipoles from the electrostatic potential
    • COI: 1:CAS:528:DC%2BC3sXhvFWqtr7O
    • Kramer C, Bereau T, Spinn A, Liedl KR, Gedeck P, Meuwly M (2013) Deriving static atomic multipoles from the electrostatic potential. J Chem Inf Model 53(12):3410–3417. doi:10.1021/ci400548w
    • (2013) J Chem Inf Model , vol.53 , Issue.12 , pp. 3410-3417
    • Kramer, C.1    Bereau, T.2    Spinn, A.3    Liedl, K.R.4    Gedeck, P.5    Meuwly, M.6
  • 29
    • 23844489887 scopus 로고    scopus 로고
    • An analytical, variable resolution, complete description of static molecules and their intermolecular binding properties
    • COI: 1:CAS:528:DC%2BD2MXktVKlsLg%3D
    • Lin JH, Clark T (2005) An analytical, variable resolution, complete description of static molecules and their intermolecular binding properties. J Chem Inf Model 45(4):1010–1016. doi:10.1021/ci050059v
    • (2005) J Chem Inf Model , vol.45 , Issue.4 , pp. 1010-1016
    • Lin, J.H.1    Clark, T.2
  • 30
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • COI: 1:CAS:528:DC%2BD3cXlsVylt78%3D
    • Wang JM, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21(12):1049–1074. doi:10.1002/1096-987x(200009)21
    • (2000) J Comput Chem , vol.21 , Issue.12 , pp. 1049-1074
    • Wang, J.M.1    Cieplak, P.2    Kollman, P.A.3
  • 31
    • 84986516411 scopus 로고
    • Application of the multimolecule and multiconformational resp methodology to biopolymers: charge derivation for DNA, RNA, and proteins
    • COI: 1:CAS:528:DyaK2MXovVKqtrY%3D
    • Cieplak P, Cornell WD, Bayly C, Kollman PA (1995) Application of the multimolecule and multiconformational resp methodology to biopolymers: charge derivation for DNA, RNA, and proteins. J Comput Chem 16(11):1357–1377
    • (1995) J Comput Chem , vol.16 , Issue.11 , pp. 1357-1377
    • Cieplak, P.1    Cornell, W.D.2    Bayly, C.3    Kollman, P.A.4
  • 32
    • 0242663237 scopus 로고    scopus 로고
    • A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
    • COI: 1:CAS:528:DC%2BD3sXovVygsbc%3D
    • Duan Y, Wu C, Chowdhury S, Lee MC, Xiong G, Zhang W, Yang R, Cieplak P, Luo R, Lee T, Caldwell J, Wang J, Kollman P (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24(16):1999–2012. doi:10.1002/jcc.10349
    • (2003) J Comput Chem , vol.24 , Issue.16 , pp. 1999-2012
    • Duan, Y.1    Wu, C.2    Chowdhury, S.3    Lee, M.C.4    Xiong, G.5    Zhang, W.6    Yang, R.7    Cieplak, P.8    Luo, R.9    Lee, T.10    Caldwell, J.11    Wang, J.12    Kollman, P.13
  • 33
    • 79959999377 scopus 로고    scopus 로고
    • R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments
    • COI: 1:CAS:528:DC%2BC3MXosVOmsbY%3D
    • Vanquelef E, Simon S, Marquant G, Garcia E, Klimerak G, Delepine JC, Cieplak P, Dupradeau FY (2011) R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments. Nucleic Acids Res 39:W511–517. doi:10.1093/nar/gkr288
    • (2011) Nucleic Acids Res , vol.39 , pp. W511-W517
    • Vanquelef, E.1    Simon, S.2    Marquant, G.3    Garcia, E.4    Klimerak, G.5    Delepine, J.C.6    Cieplak, P.7    Dupradeau, F.Y.8
  • 35
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
    • COI: 1:CAS:528:DyaK3sXlvVyqsLs%3D
    • Bayly CI, Cieplak P, Cornell WD, Kollman PA (1993) A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model. J Phys Chem 97(40):10269–10280
    • (1993) J Phys Chem , vol.97 , Issue.40 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 38
    • 2942532422 scopus 로고    scopus 로고
    • Development and testing of a general Amber force field
    • COI: 1:CAS:528:DC%2BD2cXksFakurc%3D
    • Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general Amber force field. J Comput Chem 25:1157–1174
    • (2004) J Comput Chem , vol.25 , pp. 1157-1174
    • Wang, J.1    Wolf, R.M.2    Caldwell, J.W.3    Kollman, P.A.4    Case, D.A.5
  • 39
    • 0004016501 scopus 로고
    • Coomparison of simple potential functions for simulating liquid water
    • COI: 1:CAS:528:DyaL3sXksF2htL4%3D
    • Jorgensen WL, Chandrasekhar J, Madura J, Klein ML (1983) Coomparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935
    • (1983) J Chem Phys , vol.79 , pp. 926-935
    • Jorgensen, W.L.1    Chandrasekhar, J.2    Madura, J.3    Klein, M.L.4
  • 40
    • 0038037859 scopus 로고    scopus 로고
    • Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core
    • COI: 1:CAS:528:DC%2BD3sXks1Wqsrk%3D
    • Furukawa H, Gouaux E (2003) Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core. EMBO J 22(12):2873–2885. doi:10.1093/emboj/cdg303
    • (2003) EMBO J , vol.22 , Issue.12 , pp. 2873-2885
    • Furukawa, H.1    Gouaux, E.2
  • 41
    • 13844290685 scopus 로고    scopus 로고
    • Structure of the Thermus thermophilus putative periplasmic glutamate/glutamine-binding protein
    • Takahashi H, Inagaki E, Kuroishi C, Tahirov TH (2004) Structure of the Thermus thermophilus putative periplasmic glutamate/glutamine-binding protein. Acta Crystallogr D Biol Crystallogr 60(Pt 10):1846–1854. doi:10.1107/S0907444904019420
    • (2004) Acta Crystallogr D Biol Crystallogr , vol.60 , pp. 1846-1854
    • Takahashi, H.1    Inagaki, E.2    Kuroishi, C.3    Tahirov, T.H.4
  • 43
    • 35348938968 scopus 로고    scopus 로고
    • Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase
    • COI: 1:CAS:528:DC%2BD2sXhtFOjt7bL
    • Watanabe K, Toh Y, Suto K, Shimizu Y, Oka N, Wada T, Tomita K (2007) Protein-based peptide-bond formation by aminoacyl-tRNA protein transferase. Nature 449(7164):867–871. doi:10.1038/nature06167
    • (2007) Nature , vol.449 , Issue.7164 , pp. 867-871
    • Watanabe, K.1    Toh, Y.2    Suto, K.3    Shimizu, Y.4    Oka, N.5    Wada, T.6    Tomita, K.7
  • 44
    • 84912058933 scopus 로고    scopus 로고
    • Sybyl7.3 (1991–2008). Tripos, St. Louis, MO
    • Sybyl7.3 (1991–2008). Tripos, St. Louis, MO
  • 46
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes
    • COI: 1:CAS:528:DyaE2sXktVGhsL4%3D
    • Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23:327–341
    • (1977) J Comput Phys , vol.23 , pp. 327-341
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 47
    • 84880022273 scopus 로고    scopus 로고
    • PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data
    • COI: 1:CAS:528:DC%2BC3sXptFehtr8%3D
    • Roe DR, Cheatham TE (2013) PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 9(7):3084–3095. doi:10.1021/ct400341p
    • (2013) J Chem Theory Comput , vol.9 , Issue.7 , pp. 3084-3095
    • Roe, D.R.1    Cheatham, T.E.2
  • 49
    • 0029878720 scopus 로고    scopus 로고
    • VMD: visual molecular dynamics
    • COI: 1:CAS:528:DyaK28Xis12nsrg%3D
    • Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graph Model 14(1):33–38. doi:10.1016/0263-7855(96)00018-5
    • (1996) J Mol Graph Model , vol.14 , Issue.1 , pp. 33-38
    • Humphrey, W.1    Dalke, A.2    Schulten, K.3
  • 50
    • 2442480826 scopus 로고    scopus 로고
    • Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model
    • COI: 1:CAS:528:DC%2BD2cXjvFemtL8%3D
    • Lee MC, Duan Y (2004) Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model. Proteins 55(3):620–634. doi:10.1002/prot.10470
    • (2004) Proteins , vol.55 , Issue.3 , pp. 620-634
    • Lee, M.C.1    Duan, Y.2
  • 51
    • 84970598801 scopus 로고
    • The Kerr effect of amino acids in water
    • COI: 1:CAS:528:DyaL3MXkt1eh
    • Khanarian G, Moore WJ (1980) The Kerr effect of amino acids in water. Aust J Chem 33:1727–1741
    • (1980) Aust J Chem , vol.33 , pp. 1727-1741
    • Khanarian, G.1    Moore, W.J.2
  • 52
    • 44049109576 scopus 로고
    • The glycine zwitterion does not exist in the gas phase: results from a detailed ab initio electronic structure study
    • COI: 1:CAS:528:DyaK3sXhtFSjtro%3D
    • Ding Y, Krogh-Jespersen K (1992) The glycine zwitterion does not exist in the gas phase: results from a detailed ab initio electronic structure study. Chem Phys Lett 199(3–4):261–266. doi:10.1016/0009-2614(92)80116-S
    • (1992) Chem Phys Lett , vol.199 , Issue.3-4 , pp. 261-266
    • Ding, Y.1    Krogh-Jespersen, K.2
  • 53
    • 0030595208 scopus 로고    scopus 로고
    • Why is glycine a zwitterion in aqueous solution? A theoretical study of solvent stabilising factors
    • COI: 1:CAS:528:DyaK28XlsFegtr0%3D
    • Tortonda FR, Pascual-Ahuir JL, Silla E, Tunón I (1996) Why is glycine a zwitterion in aqueous solution? A theoretical study of solvent stabilising factors. Chem Phys Lett 260(1–2):21–26. doi:10.1016/0009-2614(96)00839-1
    • (1996) Chem Phys Lett , vol.260 , Issue.1-2 , pp. 21-26
    • Tortonda, F.R.1    Pascual-Ahuir, J.L.2    Silla, E.3    Tunón, I.4
  • 54
    • 0002696495 scopus 로고    scopus 로고
    • Vibrational analysis of glycine zwitterion—an ab initio study
    • COI: 1:CAS:528:DyaK1cXlvVGjsbY%3D
    • Chakraborty D, Manogaran S (1998) Vibrational analysis of glycine zwitterion—an ab initio study. Chem Phys Lett 294(1–3):56–64. doi:10.1016/S0009-2614(98)00836-7
    • (1998) Chem Phys Lett , vol.294 , Issue.1-3 , pp. 56-64
    • Chakraborty, D.1    Manogaran, S.2
  • 55
    • 0037441479 scopus 로고    scopus 로고
    • Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine “dipeptides” (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution
    • COI: 1:CAS:528:DC%2BD3sXpvVKlsQ%3D%3D
    • Hu H, Elstner M, Hermans J (2003) Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine “dipeptides” (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Proteins 50(3):451–463. doi:10.1002/prot.10279
    • (2003) Proteins , vol.50 , Issue.3 , pp. 451-463
    • Hu, H.1    Elstner, M.2    Hermans, J.3
  • 56
    • 77956958796 scopus 로고    scopus 로고
    • Sun J, Bousquet D, Forbert H, Marx D Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics. J Chem Phys 133 (11):114508
    • Sun J, Bousquet D, Forbert H, Marx D Glycine in aqueous solution: solvation shells, interfacial water, and vibrational spectroscopy from ab initio molecular dynamics. J Chem Phys 133 (11):114508. doi:10.1063/1.3481576
  • 58
    • 33644753023 scopus 로고    scopus 로고
    • AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine
    • COI: 1:CAS:528:DC%2BD28XktVGjsrs%3D
    • Homeyer N, Horn AHC, Lanig H, Sticht H (2006) AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine. J Mol Model 12(3):281–289. doi:10.1007/s00894-005-0028-4
    • (2006) J Mol Model , vol.12 , Issue.3 , pp. 281-289
    • Homeyer, N.1    Horn, A.H.C.2    Lanig, H.3    Sticht, H.4
  • 59
    • 33846676738 scopus 로고    scopus 로고
    • Multipole electrostatic potential derived atomic charges in NDDO-methods with spd-basis sets
    • COI: 1:CAS:528:DC%2BD2sXisFantb8%3D
    • Horn AHC, Clark T (2007) Multipole electrostatic potential derived atomic charges in NDDO-methods with spd-basis sets. J Mol Model 13(2):381–392. doi:10.1007/s00894-006-0137-8
    • (2007) J Mol Model , vol.13 , Issue.2 , pp. 381-392
    • Horn, A.H.C.1    Clark, T.2
  • 60
    • 84912124683 scopus 로고    scopus 로고
    • Bryce RA The University of Manchester
    • Bryce RA The University of Manchester. http://www.pharmacy.manchester.ac.uk/bryce/amber/
  • 61
    • 84988053694 scopus 로고
    • An all atom force field for simulation of proteins and nucleic acids
    • COI: 1:CAS:528:DyaL28XhvVarsLY%3D
    • Weiner SJ, Kollman PA, Nguyen DT, Case DA (1986) An all atom force field for simulation of proteins and nucleic acids. J Comput Chem 7(2):230–252. doi:10.1002/jcc.540070216
    • (1986) J Comput Chem , vol.7 , Issue.2 , pp. 230-252
    • Weiner, S.J.1    Kollman, P.A.2    Nguyen, D.T.3    Case, D.A.4


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