메뉴 건너뛰기




Volumn 26, Issue 2, 2012, Pages 215-232

Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir

Author keywords

Amprenavir; Drug resistance; HIV 1 PR; MM PBSA; Normal mode analysis

Indexed keywords

DRUG INTERACTIONS; DRUG THERAPY; FREE ENERGY; PROTONATION; SOLVATION; VAN DER WAALS FORCES;

EID: 84861672533     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-012-9550-5     Document Type: Article
Times cited : (48)

References (66)
  • 2
    • 0001650127 scopus 로고
    • Human immunodeficiency virus has an aspartic-type protease that can be inhibited by pepstatin A
    • Seelmeir S, Schmidt H, Turk V, Von Der Helm K (1988) Human immunodeficiency virus has an aspartic-type protease that can be inhibited by pepstatin A. Proc Natl Acad Sci USA 85:6612-6616
    • (1988) Proc Natl Acad Sci USA , vol.85 , pp. 6612-6616
    • Seelmeir, S.1    Schmidt, H.2    Turk, V.3    Von Der Helm, K.4
  • 3
    • 0023829221 scopus 로고
    • Processing protease and reverse transcriptase from human immunodeficiency virus type I polyprotein in Escherichia coli
    • Mous J, Heimer EP, Le Grice SJJ (1988) Processing protease and reverse transcriptase from human immunodeficiency virus type I polyprotein in Escherichia coli. J Virol 62:1433-1436 (Pubitemid 18082959)
    • (1988) Journal of Virology , vol.62 , Issue.4 , pp. 1433-1436
    • Mous, J.1    Heimer, E.P.2    Le Grice, S.F.J.3
  • 5
    • 33847126878 scopus 로고    scopus 로고
    • Binding pathways of ligands to HIV-1 Protease: Coarse-grained and atomistic simulations
    • DOI 10.1111/j.1747-0285.2007.00464.x
    • Chang CA, Trylska J, Tozzini V, McCammon JA (2007) Binding pathways of ligands to HIV-1 protease: corase-grained and atomistic simulations. Chem Biol Drug Des 69:5-13 (Pubitemid 46277781)
    • (2007) Chemical Biology and Drug Design , vol.69 , Issue.1 , pp. 5-13
    • Chang, C.-E.A.1    Trylska, J.2    Tozzini, V.3    Andrew McCammon, J.4
  • 6
    • 33847791634 scopus 로고    scopus 로고
    • Superior virological response to boosted protease inhibitor-based highly active antiretroviral therapy in an observational treatment programme
    • DOI 10.1111/j.1468-1293.2007.00430.x
    • Wood E, Hogg RS, Yip B, Moore D, Harringan PR, Montaner JS (2007) Superior virological response to boosted protease inhibitor-based highly active antiretroviral therapy in an observational treatment programme. HIV Med 8:80-85 (Pubitemid 46390843)
    • (2007) HIV Medicine , vol.8 , Issue.2 , pp. 80-85
    • Wood, E.1    Hogg, R.S.2    Yip, B.3    Moore, D.4    Harrigan, P.R.5    Montaner, J.S.G.6
  • 7
    • 44049108744 scopus 로고    scopus 로고
    • Toward an AIDS vaccine
    • DOI 10.1126/science.1152622
    • Walker BD, Burton DR (2008) Toward an AIDS vaccine. Science 320:760-764 (Pubitemid 351929619)
    • (2008) Science , vol.320 , Issue.5877 , pp. 760-764
    • Walker, B.D.1    Burton, D.R.2
  • 8
    • 33846798356 scopus 로고    scopus 로고
    • Hydrophobic sliding: A possible mechanism for drug resistance in human immunodeficiency virus type 1 protease
    • DOI 10.1016/j.str.2007.01.006, PII S0969212607000354
    • Foulkes-Murzycki JE, Scott WR, Schiffer CA (2007) Hydrophobic sliding: a possible mechanism for drug resistance in human immunodeficiency virus type 1 protease. Structure 15:225-233 (Pubitemid 46209819)
    • (2007) Structure , vol.15 , Issue.2 , pp. 225-233
    • Foulkes-Murzycki, J.E.1    Scott, W.R.P.2    Schiffer, C.A.3
  • 9
    • 48449083017 scopus 로고    scopus 로고
    • HIV-1 drug resistance mutations: An updated framework for the second decade of HAART
    • Shafer RW, Schapiro JM (2008) HIV-1 drug resistance mutations: an updated framework for the second decade of HAART. AIDS Rev 10:67-84
    • (2008) AIDS Rev , vol.10 , pp. 67-84
    • Shafer, R.W.1    Schapiro, J.M.2
  • 11
    • 77956326486 scopus 로고    scopus 로고
    • Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters
    • Shen C-H, Wang Y-F, Kovalevsky AY, Harrison RW, Weber IT (2010) Amprenavir complexes with HIV-1 protease and its drug-resistant mutants altering hydrophobic clusters. FEBS J 277: 3699-3714
    • (2010) FEBS J , vol.277 , pp. 3699-3714
    • Shen, C.-H.1    Wang, Y.-F.2    Kovalevsky, A.Y.3    Harrison, R.W.4    Weber, I.T.5
  • 12
    • 0038184354 scopus 로고    scopus 로고
    • HIV-1 protease: Mechanism and drug discovery
    • Brik A, Wong CH (2003) HIV-1 protease: mechanism and drug discovery. Org Biomol Chem 1:5-14
    • (2003) Org Biomol Chem , vol.1 , pp. 5-14
    • Brik, A.1    Wong, C.H.2
  • 13
    • 0029859529 scopus 로고    scopus 로고
    • Ionization states of the catalytic residues in HIV-1 protease
    • DOI 10.1038/nsb1196-946
    • Smith R, Brereton IM, Chai RY, Kent SBH (1996) Ionization states of the catalytic residues in HIV-1 protease. Nat Struct Biol 3:946-950 (Pubitemid 26398328)
    • (1996) Nature Structural Biology , vol.3 , Issue.11 , pp. 946-950
    • Smith, R.1    Brereton, I.M.2    Chai, R.Y.3    Kent, S.B.H.4
  • 14
    • 68949194753 scopus 로고    scopus 로고
    • Insights into the functional role of protonation states in the HIV-1 protease-BEA369 complex: Molecular dynamics simulations and free energy calculations
    • Chen J, Yang M, Hu G, Shi S, Yi C, Zhang Q (2009) Insights into the functional role of protonation states in the HIV-1 protease-BEA369 complex: molecular dynamics simulations and free energy calculations. J Mol Model 15:1245-1252
    • (2009) J Mol Model , vol.15 , pp. 1245-1252
    • Chen, J.1    Yang, M.2    Hu, G.3    Shi, S.4    Yi, C.5    Zhang, Q.6
  • 15
    • 0029065893 scopus 로고
    • Relative binding free energies of peptide inhibitors of HIV-1 protease: The influence of the active site protonation state
    • Chen X, Tropsha A (1995) Relative binding free energies of peptide inhibitors of HIV-1 protease: the influence of the active site protonation state. J Med Chem 38:42-48
    • (1995) J Med Chem , vol.38 , pp. 42-48
    • Chen, X.1    Tropsha, A.2
  • 17
    • 40549107752 scopus 로고    scopus 로고
    • Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors
    • DOI 10.1002/jcc.20821
    • Wittayanarakul K, Hannongbua S, Feig M (2008) Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors. J Comput Chem 29:673-685 (Pubitemid 351364842)
    • (2008) Journal of Computational Chemistry , vol.29 , Issue.5 , pp. 673-685
    • Wittayanarakul, K.1    Hannongbua, S.2    Feig, M.3
  • 19
    • 0034602373 scopus 로고    scopus 로고
    • Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model
    • Wang W, Kollman PA (2000) Free energy calculations on dimer stability of the HIV protease using molecular dynamics and a continuum solvent model. J Mol Biol 303:567-582
    • (2000) J Mol Biol , vol.303 , pp. 567-582
    • Wang, W.1    Kollman, P.A.2
  • 20
    • 77951229364 scopus 로고    scopus 로고
    • Insights into drug resistance of mutations D30N and I50V to HIV-1 protease inhibitor TMC-114: Free energy calculation and molecular dynamic simulation
    • Chen J, Zhang S, Liu X, Zhang Q (2010) Insights into drug resistance of mutations D30N and I50V to HIV-1 protease inhibitor TMC-114: free energy calculation and molecular dynamic simulation. J Mol Model 16:459-468
    • (2010) J Mol Model , vol.16 , pp. 459-468
    • Chen, J.1    Zhang, S.2    Liu, X.3    Zhang, Q.4
  • 22
    • 20244387096 scopus 로고    scopus 로고
    • Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments
    • DOI 10.1128/JVI.77.8.4836-4847.2003
    • Wu TD, Schiffer CA, Gonzales MJ, Taylor J, Kantor R, Chou S, Israelski D, Zolopa AR, Fessel WJ, Shafer RW (2003) Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol 77:4836-4847 (Pubitemid 36402833)
    • (2003) Journal of Virology , vol.77 , Issue.8 , pp. 4836-4847
    • Wu, T.D.1    Schiffer, C.A.2    Gonzales, M.J.3    Taylor, J.4    Kantor, R.5    Chou, S.6    Israelski, D.7    Zolopa, A.R.8    Fessel, W.J.9    Shafer, R.W.10
  • 25
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman PA (1993) Free energy calculations: applications to chemical and biochemical phenomena. Chem Rev 93:2395-2417
    • (1993) Chem Rev , vol.93 , pp. 2395-2417
    • Kollman, P.A.1
  • 26
    • 0022666945 scopus 로고
    • Theoretical calculation of relative binding affinity in host-guest systems
    • Lybrand T, McCammon JA, Wipff G (1986) Theoretical calculation of relative binding affinity in host-guest systems. Proc Natl Acad Sci USA 83:833-835
    • (1986) Proc Natl Acad Sci USA , vol.83 , pp. 833-835
    • Lybrand, T.1    McCammon, J.A.2    Wipff, G.3
  • 27
    • 0032556243 scopus 로고    scopus 로고
    • Free energy analysis of the conformational preferences of A and B forms of DNA in solution
    • DOI 10.1021/ja981307p
    • Jayaram B, Sprous D, Young MA, Beveridge DL (1998) Free energy analysis of the conformational preferences of A and B forms of DNA in solution. J Am Chem Soc 120:10629-10633 (Pubitemid 28498806)
    • (1998) Journal of the American Chemical Society , vol.120 , Issue.41 , pp. 10629-10633
    • Jayaram, B.1    Sprous, D.2    Young, M.A.3    Beveridge, D.L.4
  • 28
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
    • DOI 10.1002/(SICI)1097-0134(19980901)32:4<399::AID-PROT1>3.0.CO;2-C
    • Vorobjev YN, Almagro JC, Hermans J (1998) Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins 32:399-413 (Pubitemid 28380782)
    • (1998) Proteins: Structure, Function and Genetics , vol.32 , Issue.4 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 29
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • DOI 10.1021/ar000033j
    • Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, Chong L, Lee M, Lee T, Duan Y, Wang W, Donini O, Cieplak P, Srinivasan J, Case DA, Cheatham TE (2000) Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc Chem Res 33:889-897 (Pubitemid 32056774)
    • (2000) Accounts of Chemical Research , vol.33 , Issue.12 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5    Chong, L.6    Lee, M.7    Lee, T.8    Duan, Y.9    Wang, W.10    Donini, O.11
  • 30
    • 84961980685 scopus 로고    scopus 로고
    • Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
    • Kuhn B, Kollman PA (2000) Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J Med Chem 43:3786-3791
    • (2000) J Med Chem , vol.43 , pp. 3786-3791
    • Kuhn, B.1    Kollman, P.A.2
  • 31
    • 76249112547 scopus 로고    scopus 로고
    • Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA
    • Rastelli G, Rio AD, Degliesposti G, Sgobba M (2010) Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. J. Comput. Chem. 31:797-810
    • (2010) J. Comput. Chem. , vol.31 , pp. 797-810
    • Rastelli, G.1    Rio, A.D.2    Degliesposti, G.3    Sgobba, M.4
  • 32
    • 0034614387 scopus 로고    scopus 로고
    • Investigating the binding specificity of U1A-RNA by computational mutagenesis
    • DOI 10.1006/jmbi.1999.3319
    • Reyes CM, Kollman PA (2000) Investigating the binding specificity of U1A-RNA by computational mutagenesis. J Mol Biol 295:1-6 (Pubitemid 30025896)
    • (2000) Journal of Molecular Biology , vol.295 , Issue.1 , pp. 1-6
    • Reyes, C.M.1    Kollman, P.A.2
  • 33
    • 0034646574 scopus 로고    scopus 로고
    • Structure and thermodynamics of RNA-protein binding: Using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change
    • Reyes CM, Kollman PA (2000) Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change. J Mol Biol 297:1145-1158
    • (2000) J Mol Biol , vol.297 , pp. 1145-1158
    • Reyes, C.M.1    Kollman, P.A.2
  • 34
    • 10944234802 scopus 로고    scopus 로고
    • Molecular dynamics simulations of 14 HIV protease mutants in complexes with indinavir
    • DOI 10.1007/s00894-004-0205-x
    • Chen X, Weber IT, Harrison RW (2004) Molecular dynamics simulations of 14 HIV protease mutants in complexes with indinavir. J Mol Model 10:373-381 (Pubitemid 40012066)
    • (2004) Journal of Molecular Modeling , vol.10 , Issue.5-6 , pp. 373-381
    • Chen, X.1    Weber, I.T.2    Harrison, R.W.3
  • 35
    • 42449147045 scopus 로고    scopus 로고
    • Evaluating the potency of HIV-1 protease drugs to combat resistance
    • Hou T, McLaughlin WA, Wang W (2007) Evaluating the potency of HIV-1 protease drugs to combat resistance. Proteins 71:1163-1174
    • (2007) Proteins , vol.71 , pp. 1163-1174
    • Hou, T.1    McLaughlin, W.A.2    Wang, W.3
  • 36
    • 39749152456 scopus 로고    scopus 로고
    • Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases
    • DOI 10.1021/ja0779250
    • Stoica I, Sadiq SK, Coveney PV (2008) Rapid and accurate prediction of binding free energies for saquinavir-bound HIV-1 proteases. J Am Chem Soc 130:2639-2648 (Pubitemid 351304779)
    • (2008) Journal of the American Chemical Society , vol.130 , Issue.8 , pp. 2639-2648
    • Stoica, I.1    Sadiq, S.K.2    Coveney, P.V.3
  • 37
    • 72049127781 scopus 로고    scopus 로고
    • Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations
    • Hu GD, Zhu T, Zhang SL, Wang D, Zhang QG (2010) Some insights into mechanism for binding and drug resistance of wild type and I50V V82A and I84V mutations in HIV-1 protease with GRL-98065 inhibitor from molecular dynamic simulations. Eur J Med Chem 45:227-235
    • (2010) Eur J Med Chem , vol.45 , pp. 227-235
    • Hu, G.D.1    Zhu, T.2    Zhang, S.L.3    Wang, D.4    Zhang, Q.G.5
  • 38
    • 77951133082 scopus 로고    scopus 로고
    • Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV
    • Cai Y, Schiffer CA (2010) Decomposing the energetic impact of drug resistant mutations in HIV-1 protease on binding DRV. J Chem Theory Comput 6:1358-1368
    • (2010) J Chem Theory Comput , vol.6 , pp. 1358-1368
    • Cai, Y.1    Schiffer, C.A.2
  • 39
    • 33947644064 scopus 로고    scopus 로고
    • Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: Mechanism for binding and drug resistance
    • DOI 10.1021/jm0609162
    • Hou T, Yu R (2007) Molecular dynamics and free energy studies on the wild-type and double mutant HIV-1 protease complexed with amprenavir and two amprenavir-related inhibitors: mechanism for binding and drug resistance. J Med Chem 50:1177-1188 (Pubitemid 46496318)
    • (2007) Journal of Medicinal Chemistry , vol.50 , Issue.6 , pp. 1177-1188
    • Hou, T.1    Yu, R.2
  • 40
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
    • DOI 10.1021/ja003834q
    • Wang J, Morin P, Wang W, Kollman PA (2001) Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J Am Chem Soc 123:5221-5230 (Pubitemid 32910665)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.22 , pp. 5221-5230
    • Wang, J.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 41
    • 78649668571 scopus 로고    scopus 로고
    • Focus on composition and interaction potential of single-pass transmembrane domains
    • Worch R, Bökel C, Höfinger S, Schwille P, Weidemann T (2010) Focus on composition and interaction potential of single-pass transmembrane domains. Proteomics 10:4196-4208
    • (2010) Proteomics , vol.10 , pp. 4196-4208
    • Worch, R.1    Bökel, C.2    Höfinger, S.3    Schwille, P.4    Weidemann, T.5
  • 45
    • 0036890178 scopus 로고    scopus 로고
    • Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
    • DOI 10.1002/jcc.10128
    • Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23:1623-1641 (Pubitemid 35330860)
    • (2002) Journal of Computational Chemistry , vol.23 , Issue.16 , pp. 1623-1641
    • Jakalian, A.1    Jack, D.B.2    Bayly, C.I.3
  • 46
    • 33748538349 scopus 로고    scopus 로고
    • Automatic atom type and bond type perception in molecular mechanical calculations
    • DOI 10.1016/j.jmgm.2005.12.005, PII S1093326305001737
    • Wang J, Wang W, Kollman PA, Case DA (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Gra Model 25:247-260 (Pubitemid 44363172)
    • (2006) Journal of Molecular Graphics and Modelling , vol.25 , Issue.2 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4
  • 48
    • 79958833423 scopus 로고    scopus 로고
    • Importance of polar solvation for cross-reactivity of antibody and its variants with steroids
    • Kar P, Lipowsky R, Knecht V (2011) Importance of polar solvation for cross-reactivity of antibody and its variants with steroids. J Phys Chem B 115:7661-7669
    • (2011) J Phys Chem B , vol.115 , pp. 7661-7669
    • Kar, P.1    Lipowsky, R.2    Knecht, V.3
  • 50
    • 33646940952 scopus 로고
    • Numerical integration of the cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
    • 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
  • 51
    • 33846823909 scopus 로고
    • Particle mesh Ewald - An Nlog(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L (1993) Particle mesh Ewald - an Nlog(N) method for Ewald sums in large systems. J Chem Phys 98:10089-10092
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 52
    • 32844457567 scopus 로고
    • Accurate calculation of hydration free energies using macroscopic solvent models
    • Sitkoff D, Sharp KA, Honig B (1994) Accurate calculation of hydration free energies using macroscopic solvent models. J Phys Chem 98:1978-1988
    • (1994) J Phys Chem , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 53
    • 0000408363 scopus 로고    scopus 로고
    • Fast, approximate algorithm for detection of solvent-inaccessible atoms
    • Weise J, Shenkin PS, Still WC (1999) Fast, approximate algorithm for detection of solvent-inaccessible atoms. J Comput Chem 20:217-230
    • (1999) J Comput Chem , vol.20 , pp. 217-230
    • Weise, J.1    Shenkin, P.S.2    Still, W.C.3
  • 54
    • 0347949637 scopus 로고    scopus 로고
    • Revisiting free energy calculations: A theoretical connection to MM/PBSA and direct calculation of the association free energy
    • Swanson JM, Henchman RH, McCammon JA (2004) Revisiting free energy calculations: a theoretical connection to MM/PBSA and direct calculation of the association free energy. Biophys J 86:67-74 (Pubitemid 38067436)
    • (2004) Biophysical Journal , vol.86 , Issue.1 , pp. 67-74
    • Swanson, J.M.J.1    Henchman, R.H.2    McCammon, J.A.3
  • 55
    • 58149327312 scopus 로고    scopus 로고
    • An improved method to predict the entropy term with the MM/PBSA approach
    • Kongsted J, Ryde U (2009) An improved method to predict the entropy term with the MM/PBSA approach. J Comput Aided Mol Des 23:63-71
    • (2009) J Comput Aided Mol Des , vol.23 , pp. 63-71
    • Kongsted, J.1    Ryde, U.2
  • 56
    • 0042710087 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • DOI 10.1021/ja990935j
    • Massova I, Kollman PA (1999) Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J Am Chem Soc 36:8133-8143 (Pubitemid 29444447)
    • (1999) Journal of the American Chemical Society , vol.121 , Issue.36 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 57
    • 0043245780 scopus 로고    scopus 로고
    • Insights into protein-protein binding by free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes
    • Gohlke H, Kiel C, Case DA (2003) Insights into protein-protein binding by free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J Mol Biol 330:891-913
    • (2003) J Mol Biol , vol.330 , pp. 891-913
    • Gohlke, H.1    Kiel, C.2    Case, D.A.3
  • 61
    • 23244440384 scopus 로고    scopus 로고
    • Constant pH molecular dynamics with proton tautomerism
    • DOI 10.1529/biophysj.105.061341
    • Khandogin J, Brooks CL III (2005) Constant pH molecular dynamics with proton tautomerism. Biophys J 89:141-157 (Pubitemid 41098271)
    • (2005) Biophysical Journal , vol.89 , Issue.1 , pp. 141-157
    • Khandogin, J.1    Brooks III, C.L.2
  • 64
    • 0023434194 scopus 로고
    • Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: Implications for a mechanism of action
    • Suguna K, Padlan EA, Smith CW, Carlson WD, Davies DR (1987) Binding of a reduced peptide inhibitor to the aspartic proteinase from Rhizopus chinensis: implications for a mechanism of action. Proc Natl Acad Sci U S A 84:7009-7013
    • (1987) Proc Natl Acad Sci u S A , vol.84 , pp. 7009-7013
    • Suguna, K.1    Padlan, E.A.2    Smith, C.W.3    Carlson, W.D.4    Davies, D.R.5
  • 66
    • 77957292370 scopus 로고    scopus 로고
    • Model amyloid peptide B18 monomer and dimer studied by replica exchange molecular dynamics simulations
    • Knecht V (2010) Model amyloid peptide B18 monomer and dimer studied by replica exchange molecular dynamics simulations. J Phys Chem B 114:12701-12707
    • (2010) J Phys Chem B , vol.114 , pp. 12701-12707
    • Knecht, V.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.