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Volumn 53, Issue 2, 2013, Pages 435-451

Structural modeling of HCV NS3/4A serine protease drug-resistance mutations using end-point continuum solvation and side-chain flexibility calculations

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BINDING SITES; COMPUTATION THEORY; ECONOMIC AND SOCIAL EFFECTS; FORECASTING; GRAPH THEORY; INVERSE PROBLEMS; LIGANDS; PROTEINS; SOLVATION; VAN DER WAALS FORCES;

EID: 84874412077     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci3004754     Document Type: Article
Times cited : (4)

References (85)
  • 1
    • 0037008160 scopus 로고    scopus 로고
    • Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
    • Gohlke, H.; Klebe, G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors Angew. Chem., Int. Ed. Engl. 2002, 41, 2645-2676
    • (2002) Angew. Chem., Int. Ed. Engl. , vol.41 , pp. 2645-2676
    • Gohlke, H.1    Klebe, G.2
  • 2
    • 60349109713 scopus 로고    scopus 로고
    • Computational evaluation of protein-small molecule binding
    • Guvench, O.; MacKerell, A. D., Jr. Computational evaluation of protein-small molecule binding Curr. Opin. Struct. Biol. 2009, 19, 56-61
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 56-61
    • Guvench, O.1    Mackerell Jr., A.D.2
  • 3
    • 64049102289 scopus 로고    scopus 로고
    • Binding of small-molecule ligands to proteins: 'what you see' is not always 'what you get'
    • Mobley, D. L.; Dill, K. A. Binding of small-molecule ligands to proteins: 'what you see' is not always 'what you get' Structure 2009, 17, 489-498
    • (2009) Structure , vol.17 , pp. 489-498
    • Mobley, D.L.1    Dill, K.A.2
  • 4
    • 84857537331 scopus 로고    scopus 로고
    • Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition
    • Wereszczynski, J.; McCammon, J. A. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition Q. Rev. Biophys. 2012, 45, 1-25
    • (2012) Q. Rev. Biophys. , vol.45 , pp. 1-25
    • Wereszczynski, J.1    McCammon, J.A.2
  • 5
    • 80052851599 scopus 로고    scopus 로고
    • Scoring functions: From free-energies of binding to enrichment in virtual screening
    • Jhoti, H. Leach, A. Springer
    • Fenu, L. A.; Lewis, R. A.; Good, A. C.; Bodkin, M.; Essex, J. W. Scoring functions: from free-energies of binding to enrichment in virtual screening. In Structure-based Drug Discovery; Jhoti, H.; Leach, A., Eds.; Springer: 2007; pp 223-245.
    • (2007) Structure-based Drug Discovery , pp. 223-245
    • Fenu, L.A.1    Lewis, R.A.2    Good, A.C.3    Bodkin, M.4    Essex, J.W.5
  • 6
    • 1942471391 scopus 로고    scopus 로고
    • Assessing scoring functions for protein-ligand interactions
    • Ferrara, P.; Gohlke, H.; Price, D. J.; Klebe, G.; Brooks, C. L. Assessing scoring functions for protein-ligand interactions J. Med. Chem. 2004, 47, 3032-3047
    • (2004) J. Med. Chem. , vol.47 , pp. 3032-3047
    • Ferrara, P.1    Gohlke, H.2    Price, D.J.3    Klebe, G.4    Brooks, C.L.5
  • 8
    • 0037763817 scopus 로고    scopus 로고
    • Comparative evaluation of 11 scoring functions for molecular docking
    • Wang, R.; Lu, Y.; Wang, S. Comparative evaluation of 11 scoring functions for molecular docking J. Med. Chem. 2003, 46, 2287-2303
    • (2003) J. Med. Chem. , vol.46 , pp. 2287-2303
    • Wang, R.1    Lu, Y.2    Wang, S.3
  • 10
    • 45749138489 scopus 로고    scopus 로고
    • MM-GB/SA rescoring of docking poses in structure-based lead optimization
    • Guimarães, C. R.; Cardozo, M. MM-GB/SA rescoring of docking poses in structure-based lead optimization J. Chem. Inf. Model. 2008, 48, 958-970
    • (2008) J. Chem. Inf. Model. , vol.48 , pp. 958-970
    • Guimarães, C.R.1    Cardozo, M.2
  • 11
    • 79951996670 scopus 로고    scopus 로고
    • Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
    • Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking J. Comput. Chem. 2011, 32, 866-877
    • (2011) J. Comput. Chem. , vol.32 , pp. 866-877
    • Hou, T.1    Wang, J.2    Li, Y.3    Wang, W.4
  • 12
    • 79952588669 scopus 로고    scopus 로고
    • Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations
    • Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations J. Chem. Inf. Model. 2011, 51, 69-82
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 69-82
    • Hou, T.1    Wang, J.2    Li, Y.3    Wang, W.4
  • 13
    • 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, P. A. 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. 2000, 43, 3786-3791
    • (2000) J. Med. Chem. , vol.43 , pp. 3786-3791
    • Kuhn, B.1    Kollman, P.A.2
  • 14
    • 84887178249 scopus 로고    scopus 로고
    • Continuum Electrostatics Solvent Modeling with the Generalized Born Model
    • Feig, M. Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Chapter 6
    • Onufriev, A. Continuum Electrostatics Solvent Modeling with the Generalized Born Model. In Modeling Solvent Environments Applications to Simulations of Biomolecules; Feig, M., Ed.; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, 2010; Chapter 6, pp 127-165.
    • (2010) Modeling Solvent Environments Applications to Simulations of Biomolecules , pp. 127-165
    • Onufriev, A.1
  • 15
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. Semianalytical treatment of solvation for molecular mechanics and dynamics J. Am. Chem. Soc. 1990, 112, 6127-6129
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 16
    • 84859438966 scopus 로고    scopus 로고
    • Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies
    • Genheden, S.; Ryde, U. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies Proteins: Struct., Funct., Bioinf. 2012, 80, 1326-1342
    • (2012) Proteins: Struct., Funct., Bioinf. , vol.80 , pp. 1326-1342
    • Genheden, S.1    Ryde, U.2
  • 17
    • 26944477331 scopus 로고    scopus 로고
    • Virtual ligand screening against Escherichia coli dihydrofolate reductase: Improving docking enrichment using physics-based methods
    • Bernacki, K.; Kalyanaraman, C.; Jacobson, M. P. Virtual ligand screening against Escherichia coli dihydrofolate reductase: improving docking enrichment using physics-based methods J. Biomol. Screening 2005, 10, 675-681
    • (2005) J. Biomol. Screening , vol.10 , pp. 675-681
    • Bernacki, K.1    Kalyanaraman, C.2    Jacobson, M.P.3
  • 18
    • 33845335781 scopus 로고    scopus 로고
    • Towards predictive ligand design with free-energy based computational methods?
    • Foloppe, N.; Hubbard, R. Towards predictive ligand design with free-energy based computational methods? Curr. Med. Chem. 2006, 13, 3583-3608
    • (2006) Curr. Med. Chem. , vol.13 , pp. 3583-3608
    • Foloppe, N.1    Hubbard, R.2
  • 19
    • 79960271379 scopus 로고    scopus 로고
    • A direct comparison of the MM-GB/SA scoring procedure and free-energy perturbation calculations using carbonic anhydrase as a test case: Strengths and pitfalls of each approach
    • Guimarães, C. R. W. A direct comparison of the MM-GB/SA scoring procedure and free-energy perturbation calculations using carbonic anhydrase as a test case: strengths and pitfalls of each approach J. Chem. Theory Comput. 2011, 7, 2296-2306
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2296-2306
    • Guimarães, C.R.W.1
  • 20
    • 34249040810 scopus 로고    scopus 로고
    • Physics-based methods for studying protein-ligand interactions
    • Huang, N.; Jacobson, M. P. Physics-based methods for studying protein-ligand interactions Curr. Opin. Drug Discovery Dev. 2007, 10, 325-331
    • (2007) Curr. Opin. Drug Discovery Dev. , vol.10 , pp. 325-331
    • Huang, N.1    Jacobson, M.P.2
  • 22
    • 33244490820 scopus 로고    scopus 로고
    • Physics-based scoring of protein-ligand complexes: Enrichment of known inhibitors in large-scale virtual screening
    • Huang, N.; Kalyanaraman, C.; Irwin, J. J.; Jacobson, M. P. Physics-based scoring of protein-ligand complexes: enrichment of known inhibitors in large-scale virtual screening J. Chem. Inf. Model. 2006, 46, 243-253
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 243-253
    • Huang, N.1    Kalyanaraman, C.2    Irwin, J.J.3    Jacobson, M.P.4
  • 23
    • 33746872935 scopus 로고    scopus 로고
    • Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring
    • Lyne, P. D.; Lamb, M. L.; Saeh, J. C. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring J. Med. Chem. 2006, 49, 4805-4808
    • (2006) J. Med. Chem. , vol.49 , pp. 4805-4808
    • Lyne, P.D.1    Lamb, M.L.2    Saeh, J.C.3
  • 24
    • 79955462105 scopus 로고    scopus 로고
    • Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA
    • Genheden, S.; Nilsson, I.; Ryde, U. Binding affinities of factor Xa inhibitors estimated by thermodynamic integration and MM/GBSA J. Chem. Inf. Model. 2011, 51, 947-958
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 947-958
    • Genheden, S.1    Nilsson, I.2    Ryde, U.3
  • 25
    • 0035846166 scopus 로고    scopus 로고
    • Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system
    • Pearlman, D. A.; Charifson, P. S. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system J. Med. Chem. 2001, 44, 3417-3423
    • (2001) J. Med. Chem. , vol.44 , pp. 3417-3423
    • Pearlman, D.A.1    Charifson, P.S.2
  • 26
    • 0035593989 scopus 로고    scopus 로고
    • How accurate can molecular dynamics/linear response and Poisson-Boltzmann/solvent accessible surface calculations be for predicting relative binding affinities? Acetylcholinesterase huprine inhibitors as a test case
    • Barril, X.; Gelpí, J. L.; López, J. M.; Orozco, M.; Luque, F. J. How accurate can molecular dynamics/linear response and Poisson-Boltzmann/solvent accessible surface calculations be for predicting relative binding affinities? Acetylcholinesterase huprine inhibitors as a test case Theor. Chem. Acc. 2001, 2-9
    • (2001) Theor. Chem. Acc. , pp. 2-9
    • Barril, X.1    Gelpí, J.L.2    López, J.M.3    Orozco, M.4    Luque, F.J.5
  • 27
    • 67650997041 scopus 로고    scopus 로고
    • Virtual fragment screening: An exploration of various docking and scoring protocols for fragments using Glide
    • Kawatkar, S.; Wang, H.; Czerminski, R.; Joseph-McCarthy, D. Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide J. Comput.-Aided Mol. Des. 2009, 527-539
    • (2009) J. Comput.-Aided Mol. Des. , pp. 527-539
    • Kawatkar, S.1    Wang, H.2    Czerminski, R.3    Joseph-Mccarthy, D.4
  • 28
    • 84859444429 scopus 로고    scopus 로고
    • Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods
    • Mikulskis, P.; Genheden, S.; Rydberg, P.; Sandberg, L.; Olsen, L.; Ryde, U. Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods J. Comput.-Aided Mol. Des. 2011, 26, 527-541
    • (2011) J. Comput.-Aided Mol. Des. , vol.26 , pp. 527-541
    • Mikulskis, P.1    Genheden, S.2    Rydberg, P.3    Sandberg, L.4    Olsen, L.5    Ryde, U.6
  • 29
    • 76249085850 scopus 로고    scopus 로고
    • How to obtain statistically converged MM/GBSA results
    • Genheden, S.; Ryde, U. How to obtain statistically converged MM/GBSA results J. Comput. Chem. 2010, 31, 837-846
    • (2010) J. Comput. Chem. , vol.31 , pp. 837-846
    • Genheden, S.1    Ryde, U.2
  • 30
    • 77951997162 scopus 로고    scopus 로고
    • Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations
    • Guimarães, C. R.; Mathiowetz, A. M. Addressing limitations with the MM-GB/SA scoring procedure using the WaterMap method and free energy perturbation calculations J. Chem. Inf. Model. 2010, 50, 547-559
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 547-559
    • Guimarães, C.R.1    Mathiowetz, A.M.2
  • 33
    • 12144260229 scopus 로고    scopus 로고
    • Control of hepatitis C: A medicinal chemistry perspective
    • Gordon, C. P.; Keller, P. A. Control of hepatitis C: a medicinal chemistry perspective J. Med. Chem. 2005, 48, 1-20
    • (2005) J. Med. Chem. , vol.48 , pp. 1-20
    • Gordon, C.P.1    Keller, P.A.2
  • 34
    • 80755159054 scopus 로고    scopus 로고
    • Discovery and development of telaprevir: An NS3-4A protease inhibitor for treating genotype 1 chronic hepatitis C virus
    • Kwong, A. D.; Kauffman, R. S.; Hurter, P.; Mueller, P. Discovery and development of telaprevir: an NS3-4A protease inhibitor for treating genotype 1 chronic hepatitis C virus Nat. Biotechnol. 2011, 29, 993-1003
    • (2011) Nat. Biotechnol. , vol.29 , pp. 993-1003
    • Kwong, A.D.1    Kauffman, R.S.2    Hurter, P.3    Mueller, P.4
  • 35
    • 38949191974 scopus 로고    scopus 로고
    • Challenges in modern drug discovery: A case study of boceprevir, an HCV protease inhibitor for the treatment of hepatitis C virus infection
    • Njoroge, F. G.; Chen, K. X.; Shih, N. Y.; Piwinski, J. J. Challenges in modern drug discovery: a case study of boceprevir, an HCV protease inhibitor for the treatment of hepatitis C virus infection Acc. Chem. Res. 2008, 41, 50-59
    • (2008) Acc. Chem. Res. , vol.41 , pp. 50-59
    • Njoroge, F.G.1    Chen, K.X.2    Shih, N.Y.3    Piwinski, J.J.4
  • 36
    • 84874408100 scopus 로고    scopus 로고
    • U.S. Food and Drug Administration. (accessed May 12)
    • U.S. Food and Drug Administration. http://www.fda.gov/NewsEvents/ Newsroom/PressAnnouncements/ucm256299.htm (accessed May 12, 2012).
    • (2012)
  • 37
    • 23944506014 scopus 로고    scopus 로고
    • Global epidemiology of hepatitis C virus infection
    • Shepard, C. W.; Lyn, F.; Alter, M. J. Global epidemiology of hepatitis C virus infection Lancet Infect. Dis. 2005, 5, 558-67
    • (2005) Lancet Infect. Dis. , vol.5 , pp. 558-567
    • Shepard, C.W.1    Lyn, F.2    Alter, M.J.3
  • 38
    • 34247552946 scopus 로고    scopus 로고
    • Hepatitis C virus - Biology, host evasion strategies, and promising new therapies on the horizon
    • Qureshi, S. A. Hepatitis C virus - biology, host evasion strategies, and promising new therapies on the horizon Med. Res. Rev. 2007, 27, 353-373
    • (2007) Med. Res. Rev. , vol.27 , pp. 353-373
    • Qureshi, S.A.1
  • 39
    • 47649116685 scopus 로고    scopus 로고
    • Mapping natural polymorphisms of hepatitis C virus NS3/4A protease and antiviral resistance to inhibitors in worldwide isolates
    • Lopez-Labrador, F. X.; Moya, A.; Gonzalez-Candelas, F. Mapping natural polymorphisms of hepatitis C virus NS3/4A protease and antiviral resistance to inhibitors in worldwide isolates Antiviral Ther. 2008, 13, 481-494
    • (2008) Antiviral Ther. , vol.13 , pp. 481-494
    • Lopez-Labrador, F.X.1    Moya, A.2    Gonzalez-Candelas, F.3
  • 41
    • 78650481557 scopus 로고    scopus 로고
    • Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding
    • Romano, K. P.; Ali, A.; Royer, W. E.; Schiffer, C. A. Drug resistance against HCV NS3/4A inhibitors is defined by the balance of substrate recognition versus inhibitor binding Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 20986-20991
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 20986-20991
    • Romano, K.P.1    Ali, A.2    Royer, W.E.3    Schiffer, C.A.4
  • 42
    • 79953184315 scopus 로고    scopus 로고
    • Combined X-ray, NMR, and kinetic analyses reveal uncommon binding characteristics of the hepatitis C virus NS3-NS4A protease inhibitor BI 201335
    • Lemke, C. T.; Goudreau, N.; Zhao, S.; Hucke, O.; Thibeault, D.; Llinas-Brunet, M.; White, P. W. Combined X-ray, NMR, and kinetic analyses reveal uncommon binding characteristics of the hepatitis C virus NS3-NS4A protease inhibitor BI 201335 J. Biol. Chem. 2011, 286, 11434-11443
    • (2011) J. Biol. Chem. , vol.286 , pp. 11434-11443
    • Lemke, C.T.1    Goudreau, N.2    Zhao, S.3    Hucke, O.4    Thibeault, D.5    Llinas-Brunet, M.6    White, P.W.7
  • 43
    • 84355166397 scopus 로고    scopus 로고
    • Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435
    • Xue, W.; Pan, D.; Yang, Y.; Liu, H.; Yao, X. Molecular modeling study on the resistance mechanism of HCV NS3/4A serine protease mutants R155K, A156V and D168A to TMC435 Antiviral Res. 2012, 93, 126-137
    • (2012) Antiviral Res. , vol.93 , pp. 126-137
    • Xue, W.1    Pan, D.2    Yang, Y.3    Liu, H.4    Yao, X.5
  • 44
    • 34547927078 scopus 로고    scopus 로고
    • Phenotypic and structural analyses of hepatitis C virus NS3 protease Arg155 variants: Sensitivity to telaprevir (VX-950) and interferon alpha
    • Zhou, Y.; Muh, U.; Hanzelka, B. L.; Bartels, D. J.; Wei, Y.; Rao, B. G.; Brennan, D. L.; Tigges, A. M.; Swenson, L.; Kwong, A. D.; Lin, C. Phenotypic and structural analyses of hepatitis C virus NS3 protease Arg155 variants: sensitivity to telaprevir (VX-950) and interferon alpha J. Biol. Chem. 2007, 282, 22619-22628
    • (2007) J. Biol. Chem. , vol.282 , pp. 22619-22628
    • Zhou, Y.1    Muh, U.2    Hanzelka, B.L.3    Bartels, D.J.4    Wei, Y.5    Rao, B.G.6    Brennan, D.L.7    Tigges, A.M.8    Swenson, L.9    Kwong, A.D.10    Lin, C.11
  • 51
    • 84874421402 scopus 로고    scopus 로고
    • Accelrys: San Diego, CA, USA
    • Discovery Studio 3.1; Accelrys: San Diego, CA, USA, 2010.
    • (2010) Discovery Studio 3.1
  • 52
    • 79960244405 scopus 로고    scopus 로고
    • Predicting fragment binding poses using a combined MCSS MM-GBSA approach
    • Haider, M. K.; Bertrand, H. O.; Hubbard, R. E. Predicting fragment binding poses using a combined MCSS MM-GBSA approach J. Chem. Inf. Model. 2010, 51, 1092-1105
    • (2010) J. Chem. Inf. Model. , vol.51 , pp. 1092-1105
    • Haider, M.K.1    Bertrand, H.O.2    Hubbard, R.E.3
  • 53
    • 0037571112 scopus 로고    scopus 로고
    • Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94
    • Halgren, T. A. Merck molecular force field. I. Basis, form, scope, parameterization, and performance of MMFF94 J. Comput. Chem. 1996, 17, 490-519
    • (1996) J. Comput. Chem. , vol.17 , pp. 490-519
    • Halgren, T.A.1
  • 54
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali, A.; Blundell, T. L. Comparative protein modelling by satisfaction of spatial restraints J. Mol. Biol. 1993, 234, 779-815
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 55
    • 0041781898 scopus 로고    scopus 로고
    • Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm
    • Wu, G.; Robertson, D. H.; Brooks, C. L., III; Vieth, M. Detailed analysis of grid-based molecular docking: a case study of CDOCKER-A CHARMm-based MD docking algorithm J. Comput. Chem. 2003, 24, 1549-1562
    • (2003) J. Comput. Chem. , vol.24 , pp. 1549-1562
    • Wu, G.1    Robertson, D.H.2    Brooks Iii, C.L.3    Vieth, M.4
  • 56
    • 0141956090 scopus 로고    scopus 로고
    • Generalized born model with a simple smoothing function
    • Im, W.; Lee, M. S.; Brooks, C. L., III Generalized born model with a simple smoothing function J. Comput. Chem. 2003, 24, 1691-1702
    • (2003) J. Comput. Chem. , vol.24 , pp. 1691-1702
    • Im, W.1    Lee, M.S.2    Brooks Iii, C.L.3
  • 58
    • 0346971105 scopus 로고    scopus 로고
    • Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
    • Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks, C. L. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures J. Comput. Chem. 2003, 25, 265-284
    • (2003) J. Comput. Chem. , vol.25 , pp. 265-284
    • Feig, M.1    Onufriev, A.2    Lee, M.S.3    Im, W.4    Case, D.A.5    Brooks, C.L.6
  • 59
    • 61449194210 scopus 로고    scopus 로고
    • Binding specificity of SH2 domains: Insight from free energy simulations
    • Gan, W.; Roux, B. Binding specificity of SH2 domains: insight from free energy simulations Proteins: Struct., Funct., Bioinf. 2008, 74, 996-1007
    • (2008) Proteins: Struct., Funct., Bioinf. , vol.74 , pp. 996-1007
    • Gan, W.1    Roux, B.2
  • 61
    • 79957585828 scopus 로고    scopus 로고
    • Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases
    • Abel, R.; Salam, N. K.; Shelley, J.; Farid, R.; Friesner, R. A.; Sherman, W. Contribution of explicit solvent effects to the binding affinity of small-molecule inhibitors in blood coagulation factor serine proteases ChemMedChem 2011, 6, 1049-1066
    • (2011) ChemMedChem , vol.6 , pp. 1049-1066
    • Abel, R.1    Salam, N.K.2    Shelley, J.3    Farid, R.4    Friesner, R.A.5    Sherman, W.6
  • 62
    • 84855932239 scopus 로고    scopus 로고
    • Flexibility analysis of biomacromolecules with application to computer-aided drug design
    • Fulle, S.; Gohlke, H. Flexibility analysis of biomacromolecules with application to computer-aided drug design Methods Mol. Biol. 2012, 819, 75-91
    • (2012) Methods Mol. Biol. , vol.819 , pp. 75-91
    • Fulle, S.1    Gohlke, H.2
  • 63
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • Jacobs, D. J.; Rader, A. J.; Kuhn, L. A.; Thorpe, M. F. Protein flexibility predictions using graph theory Proteins 2001, 44, 150-165
    • (2001) Proteins , vol.44 , pp. 150-165
    • Jacobs, D.J.1    Rader, A.J.2    Kuhn, L.A.3    Thorpe, M.F.4
  • 64
    • 33646799407 scopus 로고    scopus 로고
    • Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory
    • Ahmed, A.; Gohlke, H. Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory Proteins: Struct., Funct., Bioinf. 2006, 63, 1038-1051
    • (2006) Proteins: Struct., Funct., Bioinf. , vol.63 , pp. 1038-1051
    • Ahmed, A.1    Gohlke, H.2
  • 65
    • 27744471408 scopus 로고    scopus 로고
    • Constrained geometric simulation of diffusive motion in proteins
    • Wells, S.; Menor, S.; Hespenheide, B.; Thorpe, M. F. Constrained geometric simulation of diffusive motion in proteins Phys. Biol. 2005, 2, S127-S136
    • (2005) Phys. Biol. , vol.2
    • Wells, S.1    Menor, S.2    Hespenheide, B.3    Thorpe, M.F.4
  • 66
    • 0033025809 scopus 로고    scopus 로고
    • Predicting binding energetics from structure: Looking beyond dG
    • Murphy, K. P. Predicting binding energetics from structure: looking beyond dG Med. Res. Rev. 1999, 19, 333-339
    • (1999) Med. Res. Rev. , vol.19 , pp. 333-339
    • Murphy, K.P.1
  • 67
    • 0027991081 scopus 로고
    • Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation
    • Lee, K. H.; Xie, D.; Freire, E.; Amzel, L. M. Estimation of changes in side chain configurational entropy in binding and folding: general methods and application to helix formation Proteins 1994, 20, 68-84
    • (1994) Proteins , vol.20 , pp. 68-84
    • Lee, K.H.1    Xie, D.2    Freire, E.3    Amzel, L.M.4
  • 68
    • 65549160381 scopus 로고    scopus 로고
    • Antiviral resistance and specifically targeted therapy for HCV (STAT-C)
    • Thompson, A. J.; McHutchison, J. G. Antiviral resistance and specifically targeted therapy for HCV (STAT-C) J. Viral Hepat. 2009, 16, 377-387
    • (2009) J. Viral Hepat. , vol.16 , pp. 377-387
    • Thompson, A.J.1    McHutchison, J.G.2
  • 69
    • 80755155952 scopus 로고    scopus 로고
    • Comparison of the efficiency of the LIE and MM/GBSA methods to calculate ligand-binding energies
    • Genheden, S.; Ryde, U. Comparison of the efficiency of the LIE and MM/GBSA methods to calculate ligand-binding energies J. Chem. Theory Comput. 2011, 7, 3768-3778
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 3768-3778
    • Genheden, S.1    Ryde, U.2
  • 72
    • 84863438978 scopus 로고    scopus 로고
    • Understanding the drug resistance mechanism of hepatitis C virus NS3/4A to ITMN-191 due to R155K, A156V, D168A/E mutations: A computational study
    • Pan, D.; Xue, W.; Zhang, W.; Liu, H.; Yao, X. Understanding the drug resistance mechanism of hepatitis C virus NS3/4A to ITMN-191 due to R155K, A156V, D168A/E mutations: a computational study Biochim. Biophys. Acta, Gen. Subj. 2012, 1820, 1526-1534
    • (2012) Biochim. Biophys. Acta, Gen. Subj. , vol.1820 , pp. 1526-1534
    • Pan, D.1    Xue, W.2    Zhang, W.3    Liu, H.4    Yao, X.5
  • 73
    • 77955654922 scopus 로고    scopus 로고
    • Structural characterization of the hepatitis C virus NS3 protease from genotype 3a: The basis of the genotype 1b vs. 3a inhibitor potency shift
    • Gallo, M.; Bottomley, M. J.; Pennestri, M.; Eliseo, T.; Paci, M.; Koch, U.; Bazzo, R.; Summa, V.; Carfi, A.; Cicero, D. O. Structural characterization of the hepatitis C virus NS3 protease from genotype 3a: the basis of the genotype 1b vs. 3a inhibitor potency shift Virology 2010, 405, 424-438
    • (2010) Virology , vol.405 , pp. 424-438
    • Gallo, M.1    Bottomley, M.J.2    Pennestri, M.3    Eliseo, T.4    Paci, M.5    Koch, U.6    Bazzo, R.7    Summa, V.8    Carfi, A.9    Cicero, D.O.10
  • 74
    • 84861520787 scopus 로고    scopus 로고
    • Develop and test a solvent accessible surface area-based model in conformational entropy calculations
    • Wang, J.; Hou, T. Develop and test a solvent accessible surface area-based model in conformational entropy calculations J. Chem. Inf. Model. 2012, 52, 1199-1212
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 1199-1212
    • Wang, J.1    Hou, T.2
  • 75
    • 80051775090 scopus 로고    scopus 로고
    • Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration
    • Genheden, S.; Mikulskis, P.; Hu, L.; Kongsted, J.; Soderhjelm, P.; Ryde, U. Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration J. Am. Chem. Soc. 2011, 133, 13081-13092
    • (2011) J. Am. Chem. Soc. , vol.133 , pp. 13081-13092
    • Genheden, S.1    Mikulskis, P.2    Hu, L.3    Kongsted, J.4    Soderhjelm, P.5    Ryde, U.6
  • 76
    • 33846424559 scopus 로고    scopus 로고
    • Water at biomolecular binding interfaces
    • Li, Z.; Lazaridis, T. Water at biomolecular binding interfaces Phys. Chem. Chem. Phys. 2007, 9, 573-581
    • (2007) Phys. Chem. Chem. Phys. , vol.9 , pp. 573-581
    • Li, Z.1    Lazaridis, T.2
  • 77
    • 40949163431 scopus 로고    scopus 로고
    • Role of the active-site solvent in the thermodynamics of factor Xa ligand binding
    • Abel, R.; Young, T.; Farid, R.; Berne, B. J.; Friesner, R. A. Role of the active-site solvent in the thermodynamics of factor Xa ligand binding J. Am. Chem. Soc. 2008, 130, 2817-2831
    • (2008) J. Am. Chem. Soc. , vol.130 , pp. 2817-2831
    • Abel, R.1    Young, T.2    Farid, R.3    Berne, B.J.4    Friesner, R.A.5
  • 78
    • 84856776282 scopus 로고    scopus 로고
    • Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization
    • Beuming, T.; Che, Y.; Abel, R.; Kim, B.; Shanmugasundaram, V.; Sherman, W. Thermodynamic analysis of water molecules at the surface of proteins and applications to binding site prediction and characterization Proteins 2012, 80, 871-883
    • (2012) Proteins , vol.80 , pp. 871-883
    • Beuming, T.1    Che, Y.2    Abel, R.3    Kim, B.4    Shanmugasundaram, V.5    Sherman, W.6
  • 79
    • 84863812540 scopus 로고    scopus 로고
    • Ligand binding stepwise disrupts water network in thrombin: Enthalpic and entropic changes reveal classical hydrophobic effect
    • Biela, A.; Sielaff, F.; Terwesten, F.; Heine, A.; Steinmetzer, T.; Klebe, G. Ligand binding stepwise disrupts water network in thrombin: enthalpic and entropic changes reveal classical hydrophobic effect J. Med. Chem. 2012, 55, 6094-6110
    • (2012) J. Med. Chem. , vol.55 , pp. 6094-6110
    • Biela, A.1    Sielaff, F.2    Terwesten, F.3    Heine, A.4    Steinmetzer, T.5    Klebe, G.6
  • 80
    • 0033824470 scopus 로고    scopus 로고
    • DaliLite workbench for protein structure comparison
    • Holm, L.; Park, J. DaliLite workbench for protein structure comparison Bioinformatics 2000, 16, 566-567
    • (2000) Bioinformatics , vol.16 , pp. 566-567
    • Holm, L.1    Park, J.2
  • 81
    • 0030005250 scopus 로고    scopus 로고
    • Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides
    • Wimley, W. C.; Creamer, T. P.; White, S. H. Solvation energies of amino acid side chains and backbone in a family of host-guest pentapeptides Biochemistry 1996, 35, 5109-5124
    • (1996) Biochemistry , vol.35 , pp. 5109-5124
    • Wimley, W.C.1    Creamer, T.P.2    White, S.H.3
  • 84
    • 0029864591 scopus 로고    scopus 로고
    • Direct measurement of salt-bridge solvation energies using a peptide model system: Implications for protein stability
    • Wimley, W. C.; Gawrisch, K.; Creamer, T. P.; White, S. H. Direct measurement of salt-bridge solvation energies using a peptide model system: implications for protein stability Proc. Natl. Acad. Sci. U. S. A. 1996, 93, 2985-2990
    • (1996) Proc. Natl. Acad. Sci. U. S. A. , vol.93 , pp. 2985-2990
    • Wimley, W.C.1    Gawrisch, K.2    Creamer, T.P.3    White, S.H.4
  • 85
    • 70449522914 scopus 로고    scopus 로고
    • Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site
    • Boyce, S. E.; Mobley, D. L.; Rocklin, G. J.; Graves, A. P.; Dill, K. A.; Shoichet, B. K. Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site J. Mol. Biol. 2009, 394, 747-763
    • (2009) J. Mol. Biol. , vol.394 , pp. 747-763
    • Boyce, S.E.1    Mobley, D.L.2    Rocklin, G.J.3    Graves, A.P.4    Dill, K.A.5    Shoichet, B.K.6


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