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Volumn , Issue , 2005, Pages 441-476

Principles and Methods of Docking and Ligand Design

Author keywords

Analog based design; Docking and ligand design; Genotype related drug responses

Indexed keywords

DRUG RESPONSE; LIGAND DESIGN;

EID: 4444368616     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/0471721204.ch22     Document Type: Chapter
Times cited : (3)

References (131)
  • 2
    • 0002833057 scopus 로고    scopus 로고
    • Docking small ligands in flexible binding sites
    • Apostolakis J, Pluckthun A, Caflisch A (1998): Docking small ligands in flexible binding sites. J Comp Chem 19(1):21-37.
    • (1998) J Comp Chem , vol.19 , Issue.1 , pp. 21-37
    • Apostolakis, J.1    Pluckthun, A.2    Caflisch, A.3
  • 3
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Aqvist J, Medina C, Samuelsson J-E (1994): A new method for predicting binding affinity in computer-aided drug design. Protein Eng 7(3):385-91.
    • (1994) Protein Eng , vol.7 , Issue.3 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.-E.3
  • 4
    • 0030134110 scopus 로고    scopus 로고
    • On the validity of electrostatic linear response in polar solvents
    • Aqvist J, T, Hansson (1996): On the validity of electrostatic linear response in polar solvents. J Phys Chem A 100:9512-21.
    • (1996) J Phys Chem A , vol.100 , pp. 9512-9521
    • Aqvist, J.1    Hansson, T.2
  • 7
    • 3342877839 scopus 로고    scopus 로고
    • Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function
    • Bahar I, Erman B, Jernigan RL, Atilgan AR, Covell DG (1999): Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function. J Mol Biol 285:1023-37.
    • (1999) J Mol Biol , vol.285 , pp. 1023-1037
    • Bahar, I.1    Erman, B.2    Jernigan, R.L.3    Atilgan, A.R.4    Covell, D.G.5
  • 8
    • 0000705154 scopus 로고    scopus 로고
    • Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model
    • Banks JL, Kaminski GA, Zhou RH, Mainz DT, Berne BJ, Friesner RA (1999): Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model. J Chem Phys 110(2):741-54.
    • (1999) J Chem Phys , vol.110 , Issue.2 , pp. 741-754
    • Banks, J.L.1    Kaminski, G.A.2    Zhou, R.H.3    Mainz, D.T.4    Berne, B.J.5    Friesner, R.A.6
  • 9
    • 0032533791 scopus 로고    scopus 로고
    • Flexible docking using tabu search and an empirical estimate of binding affinity
    • Baxter CA, Murray CW, Waszkowycz B, Young SS (1998): Flexible docking using tabu search and an empirical estimate of binding affinity. Proteins 33:367-82.
    • (1998) Proteins , vol.33 , pp. 367-382
    • Baxter, C.A.1    Murray, C.W.2    Waszkowycz, B.3    Young, S.S.4
  • 10
    • 3042524904 scopus 로고
    • A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESPmodel
    • Bayly CI, Cieplak P, Cornell WD, Kollman PA (1993): A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESPmodel. J Phys Chem 97:10269-80.
    • (1993) J Phys Chem , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 11
    • 0002775934 scopus 로고
    • Interaction models for water in relation to protein hydration
    • In: Pullman B, editor., Reidel:Dordrecht
    • Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J (1981): Interaction models for water in relation to protein hydration. In: Pullman B, editor. Intermolecular Forces, Reidel:Dordrecht: pp 331-42.
    • (1981) Intermolecular Forces , pp. 331-342
    • Berendsen, H.J.C.1    Postma, J.P.M.2    van Gunsteren, W.F.3    Hermans, J.4
  • 12
    • 0032897494 scopus 로고    scopus 로고
    • An analysis of conformational changes on protein-protein association: implications for predictive docking
    • Betts MJ, Sternberg MJE (1999): An analysis of conformational changes on protein-protein association: implications for predictive docking. Protein Eng 12(4):271-83.
    • (1999) Protein Eng , vol.12 , Issue.4 , pp. 271-283
    • Betts, M.J.1    Sternberg, M.J.E.2
  • 13
    • 0034649618 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations
    • Bissantz C, Folkers G, Rognan D (2000): Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem 43:4759-67.
    • (2000) J Med Chem , vol.43 , pp. 4759-4767
    • Bissantz, C.1    Folkers, G.2    Rognan, D.3
  • 14
    • 0031152087 scopus 로고    scopus 로고
    • Computational approaches for combinatorial library design and molecular diversity analysis
    • Blaney JM, Martin EJ (1997): Computational approaches for combinatorial library design and molecular diversity analysis. Curr Opin Chem Biol 1:54-9.
    • (1997) Curr Opin Chem Biol , vol.1 , pp. 54-59
    • Blaney, J.M.1    Martin, E.J.2
  • 15
    • 0032479179 scopus 로고    scopus 로고
    • Anatomy of hot spots in protein interfaces
    • Bogan AA, Thorn KS (1998): Anatomy of hot spots in protein interfaces. J Mol Biol 280(1):1-9.
    • (1998) J Mol Biol , vol.280 , Issue.1 , pp. 1-9
    • Bogan, A.A.1    Thorn, K.S.2
  • 16
    • 0028036120 scopus 로고
    • Multiple highly diverse structures complementary to enzyme binding sites: results of extensive application of de novo design method incorporating combinatorial grow
    • Bohacek RS, McMartin C (1994): Multiple highly diverse structures complementary to enzyme binding sites: results of extensive application of de novo design method incorporating combinatorial grow. J Am Chem Soc 116:5560-71.
    • (1994) J Am Chem Soc , vol.116 , pp. 5560-5571
    • Bohacek, R.S.1    McMartin, C.2
  • 17
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • Bohm H-J (1994): The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput-Aided Mol Des 8:243-56.
    • (1994) J Comput-Aided Mol Des , vol.8 , pp. 243-256
    • Bohm, H.-J.1
  • 18
    • 0038259177 scopus 로고    scopus 로고
    • Structure-based library design: molecular modelling merges with combinatorial chemistry
    • Bohm H-J, Stahl M (2000): Structure-based library design: molecular modelling merges with combinatorial chemistry. Curr Opin Chem Biol 4:283-6.
    • (2000) Curr Opin Chem Biol , vol.4 , pp. 283-286
    • Bohm, H.-J.1    Stahl, M.2
  • 19
    • 0035827113 scopus 로고    scopus 로고
    • Explicit-solvent molecular dynamics simulation at constant pH: methodology and application to small amines
    • Borjesson U, Hunenberger PH (2001): Explicit-solvent molecular dynamics simulation at constant pH: methodology and application to small amines. J Chem Phys 114(22):9706-19.
    • (2001) J Chem Phys , vol.114 , Issue.22 , pp. 9706-9719
    • Borjesson, U.1    Hunenberger, P.H.2
  • 21
    • 85080392736 scopus 로고    scopus 로고
    • CAPRI: Critical Assessment of Prediction of Interactions
    • CAPRI: Critical Assessment of Prediction of Interactions, http://capri.ebi.ac.uk.2001.
  • 22
    • 0028331255 scopus 로고
    • Normal mode analysis of protein dynamics
    • Case DA (1994): Normal mode analysis of protein dynamics. Curr Opin Struc Biol 4:285-90.
    • (1994) Curr Opin Struc Biol , vol.4 , pp. 285-290
    • Case, D.A.1
  • 23
    • 0008589609 scopus 로고    scopus 로고
    • Recent successes and continuing limitations in computer-aided drug design
    • In: Charifson PS, editor., New York: Marcel Dekker
    • Charifson PS, Kuntz ID (1997): Recent successes and continuing limitations in computer-aided drug design. In: Charifson PS, editor. Practical Application of Computer-Aided Drug Design. New York: Marcel Dekker, pp 1-37.
    • (1997) Practical Application of Computer-Aided Drug Design , pp. 1-37
    • Charifson, P.S.1    Kuntz, I.D.2
  • 24
    • 0033576680 scopus 로고    scopus 로고
    • Consensus scoring: a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
    • [Comparison of different scoring functions.]
    • Charifson PS, Corkery JJ, Murcko MA, Walters WP (1999): Consensus scoring: a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem 42:5100-9. [Comparison of different scoring functions.]
    • (1999) J Med Chem , vol.42 , pp. 5100-5109
    • Charifson, P.S.1    Corkery, J.J.2    Murcko, M.A.3    Walters, W.P.4
  • 25
    • 0035974484 scopus 로고    scopus 로고
    • Molecular mechanics models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases
    • Cieplak P, Caldwell JW, Kollman PA (2001): Molecular mechanics models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases. J Comp Chem 22(10):1048-57.
    • (2001) J Comp Chem , vol.22 , Issue.10 , pp. 1048-1057
    • Cieplak, P.1    Caldwell, J.W.2    Kollman, P.A.3
  • 26
    • 0031487738 scopus 로고    scopus 로고
    • Current issues in de novo molecular design
    • In:Lipkowitz KB, Boyd DB, editor., New York: Wiley-VCH
    • Clark DE, Murray CW, Li J (1997): Current issues in de novo molecular design. In:Lipkowitz KB, Boyd DB, editor. Reviews in Computational Chemistry. New York: Wiley-VCH, pp 66-125.
    • (1997) Reviews in Computational Chemistry , pp. 66-125
    • Clark, D.E.1    Murray, C.W.2    Li, J.3
  • 28
    • 0042139644 scopus 로고    scopus 로고
    • Comparison of generalized Born and Poisson models:energetics and dynamics of HIV protease
    • David L, Luo R, Gilson MK (2000): Comparison of generalized Born and Poisson models:energetics and dynamics of HIV protease. J Comp Chem 21:295-309.
    • (2000) J Comp Chem , vol.21 , pp. 295-309
    • David, L.1    Luo, R.2    Gilson, M.K.3
  • 29
    • 0035144771 scopus 로고    scopus 로고
    • Ligand-receptor docking with the Mining Minima optimizer
    • David L, Luo R, Gilson MK (2001): Ligand-receptor docking with the Mining Minima optimizer. J Comput-Aided Mol Des 15:157-71.
    • (2001) J Comput-Aided Mol Des , vol.15 , pp. 157-171
    • David, L.1    Luo, R.2    Gilson, M.K.3
  • 30
    • 0026124585 scopus 로고
    • Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program
    • Davis ME, Madura JD, Luty BA, McCammon JA (1991): Electrostatics and diffusion of molecules in solution: simulations with the University of Houston Brownian Dynamics program. Comput Physics Commun 62:187-97.
    • (1991) Comput Physics Commun , vol.62 , pp. 187-197
    • Davis, M.E.1    Madura, J.D.2    Luty, B.A.3    McCammon, J.A.4
  • 31
    • 0035342434 scopus 로고    scopus 로고
    • High throughput docking for library design and library prioritization
    • Diller DJ, Merz KM, Jr, (2001): High throughput docking for library design and library prioritization. Proteins 43:113-24.
    • (2001) Proteins , vol.43 , pp. 113-124
    • Diller, D.J.1    Merz, K.M.2
  • 32
    • 0028282687 scopus 로고
    • HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site
    • Eisen MB, Wiley DC, Karplus M (1994): HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site. Proteins 19:199-221.
    • (1994) Proteins , vol.19 , pp. 199-221
    • Eisen, M.B.1    Wiley, D.C.2    Karplus, M.3
  • 33
    • 6244283606 scopus 로고    scopus 로고
    • Critical evaluation of search algorithms for automated molecular docking and database screening
    • Ewing TJA, Kuntz ID (1997): Critical evaluation of search algorithms for automated molecular docking and database screening. J Comp Chem 18:1175-89.
    • (1997) J Comp Chem , vol.18 , pp. 1175-1189
    • Ewing, T.J.A.1    Kuntz, I.D.2
  • 34
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases
    • Ewing TJA, Makino S, Skillman AG, Kuntz ID (2001): DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J Comput-Aided Mol Des 15:411-28.
    • (2001) J Comput-Aided Mol Des , vol.15 , pp. 411-428
    • Ewing, T.J.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 35
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics, and biochemical information
    • Gabb HA, Jackson RM, Sternberg MJE (1997): Modelling protein docking using shape complementarity, electrostatics, and biochemical information. J Mol Biol 272:106-20.
    • (1997) J Mol Biol , vol.272 , pp. 106-120
    • Gabb, H.A.1    Jackson, R.M.2    Sternberg, M.J.E.3
  • 36
    • 0028243847 scopus 로고
    • Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries
    • Gallop MA, Barrett RW, Dower WJ, Fodor SPA, Gordon EM (1994): Applications of combinatorial technologies to drug discovery. 1. Background and peptide combinatorial libraries. J Med Chem 39(9):1233-51.
    • (1994) J Med Chem , vol.39 , Issue.9 , pp. 1233-1251
    • Gallop, M.A.1    Barrett, R.W.2    Dower, W.J.3    Fodor, S.P.A.4    Gordon, E.M.5
  • 37
    • 49149147973 scopus 로고
    • Iterative partial equalization of orbital electronegativity-rapid access to atomic charges
    • Gasteiger J, Marsili M (1980): Iterative partial equalization of orbital electronegativity-rapid access to atomic charges. Tetrahedron 36:3219-88.
    • (1980) Tetrahedron , vol.36 , pp. 3219-3288
    • Gasteiger, J.1    Marsili, M.2
  • 38
    • 0035312864 scopus 로고    scopus 로고
    • Statistical potentials and scoring functions applied to protein-ligand binding
    • Gohlke H, Klebe G (2001): Statistical potentials and scoring functions applied to protein-ligand binding. Curr Opin Struc Biol 11:231-5.
    • (2001) Curr Opin Struc Biol , vol.11 , pp. 231-235
    • Gohlke, H.1    Klebe, G.2
  • 39
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford PJ (1985): A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem 28:849-57.
    • (1985) J Med Chem , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 40
    • 0028318863 scopus 로고
    • Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions
    • Gordon EM, Barrett RW, Dower WJ, Fodor SPA, Gallop MA (1994): Applications of combinatorial technologies to drug discovery. 2. Combinatorial organic synthesis, library screening strategies, and future directions. J Med Chem 37(10):1385-1401.
    • (1994) J Med Chem , vol.37 , Issue.10 , pp. 1385-1401
    • Gordon, E.M.1    Barrett, R.W.2    Dower, W.J.3    Fodor, S.P.A.4    Gallop, M.A.5
  • 41
    • 0035971738 scopus 로고    scopus 로고
    • A smooth permittivity function for Poisson-Boltzmann solvation models
    • Grant AJ, Pickup BT, Nicholls A (2001): A smooth permittivity function for Poisson-Boltzmann solvation models. J Comp Chem 22(6):608-40.
    • (2001) J Comp Chem , vol.22 , Issue.6 , pp. 608-640
    • Grant, A.J.1    Pickup, B.T.2    Nicholls, A.3
  • 43
    • 0030120054 scopus 로고    scopus 로고
    • Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal
    • Gschwend DA, Kuntz ID (1996b) Orientational sampling and rigid-body minimization in molecular docking revisited: on-the-fly optimization and degeneracy removal. J Comput-Aided Mol Des 10:123-32.
    • (1996) J Comput-Aided Mol Des , vol.10 , pp. 123-132
    • Gschwend, D.A.1    Kuntz, I.D.2
  • 45
    • 0034081944 scopus 로고    scopus 로고
    • Evaluation of docking/scoring approaches: a comparative study based on MMP3 inhibitors
    • Ha S, Andreani R, Robbins A, Muegge I (2000): Evaluation of docking/scoring approaches: a comparative study based on MMP3 inhibitors. J Comput-Aided Mol Des 14:435-48.
    • (2000) J Comput-Aided Mol Des , vol.14 , pp. 435-448
    • Ha, S.1    Andreani, R.2    Robbins, A.3    Muegge, I.4
  • 47
    • 0003955925 scopus 로고
    • ACS Professional Reference Book, Vol. I and II. New York: Oxford University Press USA
    • Hansch C, Leo A, Hoekman DH (1995): Exploring QSAR. ACS Professional Reference Book, Vol. I and II. New York: Oxford University Press USA.
    • (1995) Exploring QSAR
    • Hansch, C.1    Leo, A.2    Hoekman, D.H.3
  • 48
    • 0031079364 scopus 로고    scopus 로고
    • "Mining minima": direct computation of conformational free energies
    • Head MS, Given JA, Gilson MK (1997): "Mining minima": direct computation of conformational free energies. J Phys Chem A 101:1609-18.
    • (1997) J Phys Chem A , vol.101 , pp. 1609-1618
    • Head, M.S.1    Given, J.A.2    Gilson, M.K.3
  • 49
    • 0032054675 scopus 로고    scopus 로고
    • Computational alchemy to calculate absolute protein-ligand binding free energy
    • Helms V, Wade RC (1998): Computational alchemy to calculate absolute protein-ligand binding free energy. J Am Chem Soc 120:2710-3.
    • (1998) J Am Chem Soc , vol.120 , pp. 2710-2713
    • Helms, V.1    Wade, R.C.2
  • 50
    • 4243067681 scopus 로고    scopus 로고
    • Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests
    • Hendsch ZS, Jonsson T, Sauer RT, Tidor B (1996): Protein stabilization by removal of unsatisfied polar groups: computational approaches and experimental tests. Biochemistry 35(24):7621-5.
    • (1996) Biochemistry , vol.35 , Issue.24 , pp. 7621-7625
    • Hendsch, Z.S.1    Jonsson, T.2    Sauer, R.T.3    Tidor, B.4
  • 52
    • 0029016182 scopus 로고
    • Classical electrostatics in biology and chemistry
    • [Review of electrostatic contributions to solvation and binding free energies.]
    • Honig B, Nicholls A (1995): Classical electrostatics in biology and chemistry. Science 268:1144-9. [Review of electrostatic contributions to solvation and binding free energies.]
    • (1995) Science , vol.268 , pp. 1144-1149
    • Honig, B.1    Nicholls, A.2
  • 53
    • 0001041959 scopus 로고    scopus 로고
    • Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
    • Jakalian A, Bush BL, Jack DB, Bayly CI (2000): Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. J Comp Chem 21(2):132-46.
    • (2000) J Comp Chem , vol.21 , Issue.2 , pp. 132-146
    • Jakalian, A.1    Bush, B.L.2    Jack, D.B.3    Bayly, C.I.4
  • 54
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones G, Willett P, Glen RC (1995): Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 245:43-53.
    • (1995) J Mol Biol , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 55
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997): Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-48.
    • (1997) J Mol Biol , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 56
  • 57
    • 0028818570 scopus 로고
    • Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding
    • Juffer AH, Eisenhaber F, Hubbard SJ, Walther D, Argos P (1995): Comparison of atomic solvation parametric sets: applicability and limitations in protein folding and binding. Protein Sci 4:2499-509.
    • (1995) Protein Sci , vol.4 , pp. 2499-2509
    • Juffer, A.H.1    Eisenhaber, F.2    Hubbard, S.J.3    Walther, D.4    Argos, P.5
  • 58
    • 0026572775 scopus 로고
    • Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA (1992):Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 89:2195-9.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 60
    • 0031581852 scopus 로고    scopus 로고
    • Molecular docking to ensembles of protein structures
    • Knegtel RMA, Kuntz ID, Oshiro CM (1997): Molecular docking to ensembles of protein structures. J Mol Biol 266(2):424-40.
    • (1997) J Mol Biol , vol.266 , Issue.2 , pp. 424-440
    • Knegtel, R.M.A.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 61
    • 0032708785 scopus 로고    scopus 로고
    • Efficacy and selectivity in flexible database docking
    • Knegtel RMA,Wagener M (1999): Efficacy and selectivity in flexible database docking. Proteins 37:334-45.
    • (1999) Proteins , vol.37 , pp. 334-345
    • Knegtel, R.M.A.1    Wagener, M.2
  • 62
    • 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 93:2395-417.
    • (1993) Chem Rev , vol.93 , pp. 2395-2417
    • Kollman, P.A.1
  • 64
    • 0033388757 scopus 로고    scopus 로고
    • Ligand docking and screening with FlexX
    • Kramer B, Metz G, Rarey M, Lengauer T (1999): Ligand docking and screening with FlexX. Med Chem Res 9(7-8):463-78.
    • (1999) Med Chem Res , vol.9 , Issue.7-8 , pp. 463-478
    • Kramer, B.1    Metz, G.2    Rarey, M.3    Lengauer, T.4
  • 65
    • 0034716751 scopus 로고    scopus 로고
    • A ligand that is predicted to bind better to avidin than biotin:insights from computational fluorine scanning
    • Kuhn B, Kollman PA (2000): A ligand that is predicted to bind better to avidin than biotin:insights from computational fluorine scanning. J Am Chem Soc 122(16):3909-16.
    • (2000) J Am Chem Soc , vol.122 , Issue.16 , pp. 3909-3916
    • Kuhn, B.1    Kollman, P.A.2
  • 66
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: dynamic landscapes and population shifts
    • Kumar S, Ma B, Tsai C, Sinha N, Nussinov R (2000): Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 9:10-9.
    • (2000) Protein Sci , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.3    Sinha, N.4    Nussinov, R.5
  • 68
    • 0031320150 scopus 로고    scopus 로고
    • Computational approaches to molecular recognition
    • Lamb MD, Jorgensen WL (1997): Computational approaches to molecular recognition. Curr Opin Chem Biol 1:449-57.
    • (1997) Curr Opin Chem Biol , vol.1 , pp. 449-457
    • Lamb, M.D.1    Jorgensen, W.L.2
  • 70
    • 0028380643 scopus 로고
    • CAVEAT-a program to facilitate the design of organic molecules
    • Lauri G, Bartlett PA (1994): CAVEAT-a program to facilitate the design of organic molecules. J Comput-Aided Mol Des 8(1):51-66.
    • (1994) J Comput-Aided Mol Des , vol.8 , Issue.1 , pp. 51-66
    • Lauri, G.1    Bartlett, P.A.2
  • 71
    • 0026570977 scopus 로고
    • CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure
    • Lawrence MC, Davis PC (1992): CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure. Proteins 12:31-41.
    • (1992) Proteins , vol.12 , pp. 31-41
    • Lawrence, M.C.1    Davis, P.C.2
  • 72
    • 0028158936 scopus 로고
    • Ligand docking to proteins with discrete side-chain flexibility
    • Leach AR (1994): Ligand docking to proteins with discrete side-chain flexibility. J Mol Biol 235:345-56.
    • (1994) J Mol Biol , vol.235 , pp. 345-356
    • Leach, A.R.1
  • 73
    • 0002015005 scopus 로고    scopus 로고
    • A survey of methods for searching the conformational space of small and medium-sized molecules
    • In: Lipkowitz KB, Boyd DB, editors., New York: Wiley-VCH
    • Leach AR (1997): A survey of methods for searching the conformational space of small and medium-sized molecules. In: Lipkowitz KB, Boyd DB, editors. Reviews in Computational Chemistry. New York: Wiley-VCH, pp 1-55.
    • (1997) Reviews in Computational Chemistry , pp. 1-55
    • Leach, A.R.1
  • 74
    • 0003653899 scopus 로고    scopus 로고
    • 2nd ed. Englewood Cliffs, NJ: Prentice Hall. [Comprehensive text on major techniques of molecular modeling and computational chemistry.]
    • Leach AR (2001): Molecular Modelling: Principles and Applications, 2nd ed. Englewood Cliffs, NJ: Prentice Hall. [Comprehensive text on major techniques of molecular modeling and computational chemistry.]
    • (2001) Molecular Modelling: Principles and Applications
    • Leach, A.R.1
  • 75
    • 0034256065 scopus 로고    scopus 로고
    • The in silico world of virtual libraries
    • Leach AR, Hann MM (2000): The in silico world of virtual libraries. Drug Discovery Today 5(8):326-36.
    • (2000) Drug Discovery Today , vol.5 , Issue.8 , pp. 326-336
    • Leach, A.R.1    Hann, M.M.2
  • 76
    • 0031310094 scopus 로고    scopus 로고
    • Packing as a structural basis of protein stability: understanding mutant properties from wildtype structure
    • Lee CE, Levitt M (1997): Packing as a structural basis of protein stability: understanding mutant properties from wildtype structure. Pacific Symp Biocomput pp 245-255.
    • (1997) Pacific Symp Biocomput , pp. 245-255
    • Lee, C.E.1    Levitt, M.2
  • 77
    • 85080411462 scopus 로고    scopus 로고
    • LEAPFROG, Sybyl Receptor-based Design v6.8, Tripos Inc., 1699 South Hanley Road, St. Louis, MO 63144
    • LEAPFROG, Sybyl Receptor-based Design v6.8, pp 1-159, Tripos Inc., 1699 South Hanley Road, St. Louis, MO 63144.
  • 78
    • 0031024171 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (1997): Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Del Rev 23:3-25.
    • (1997) Adv Drug Del Rev , vol.23 , pp. 3-25
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 79
    • 0032855301 scopus 로고    scopus 로고
    • MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
    • Liu M, Wang SM (1999): MCDOCK: A Monte Carlo simulation approach to the molecular docking problem. J Comput-Aided Mol Des 13(5):435-51.
    • (1999) J Comput-Aided Mol Des , vol.13 , Issue.5 , pp. 435-451
    • Liu, M.1    Wang, S.M.2
  • 81
    • 0035910266 scopus 로고    scopus 로고
    • Achieving stability and conformational specificity in designed proteins via binary patterning
    • Marshall SA, Mayo SL (2001): Achieving stability and conformational specificity in designed proteins via binary patterning. J Mol Biol 305(3):619-31.
    • (2001) J Mol Biol , vol.305 , Issue.3 , pp. 619-631
    • Marshall, S.A.1    Mayo, S.L.2
  • 82
    • 84986432941 scopus 로고
    • Automated docking with grid-based energy evaluation
    • Meng EC, Shoichet BK, Kuntz ID (1992): Automated docking with grid-based energy evaluation. J Comput Chem 13:505-24.
    • (1992) J Comput Chem , vol.13 , pp. 505-524
    • Meng, E.C.1    Shoichet, B.K.2    Kuntz, I.D.3
  • 83
  • 84
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: a multiple copy simultaneous search method
    • Miranker A, Karplus M (1991): Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins 11:29-34.
    • (1991) Proteins , vol.11 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 85
    • 0029586802 scopus 로고
    • An automated method for dynamic ligand design
    • Miranker A, Karplus M (1995): An automated method for dynamic ligand design. Proteins 23:472-90.
    • (1995) Proteins , vol.23 , pp. 472-490
    • Miranker, A.1    Karplus, M.2
  • 86
    • 33845377127 scopus 로고
    • Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation
    • Miyazawa S, Jernigan RL (1985): Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18:534-52.
    • (1985) Macromolecules , vol.18 , pp. 534-552
    • Miyazawa, S.1    Jernigan, R.L.2
  • 87
    • 0029919190 scopus 로고    scopus 로고
    • Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
    • Miyazawa S, Jernigan RL (1996): Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J Mol Biol 256:623-44.
    • (1996) J Mol Biol , vol.256 , pp. 623-644
    • Miyazawa, S.1    Jernigan, R.L.2
  • 88
    • 0026345685 scopus 로고
    • Computer design of bioactive molecules: a method for receptorbased de novo ligand design
    • Moon JB, Howe JW (1991): Computer design of bioactive molecules: a method for receptorbased de novo ligand design. Proteins 11:314-28.
    • (1991) Proteins , vol.11 , pp. 314-328
    • Moon, J.B.1    Howe, J.W.2
  • 90
    • 0033566211 scopus 로고    scopus 로고
    • Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein
    • Muegge I, Martin YC, Hajduk PJ, Fesik SW (1999): Evaluation of PMF scoring in docking weak ligands to the FK506 binding protein. J Med Chem 42:2498-503.
    • (1999) J Med Chem , vol.42 , pp. 2498-2503
    • Muegge, I.1    Martin, Y.C.2    Hajduk, P.J.3    Fesik, S.W.4
  • 91
    • 11644266970 scopus 로고
    • Electronic population analysis on LCAO-MO molecular wave functions I
    • Mulliken RS (1955): Electronic population analysis on LCAO-MO molecular wave functions I. J Chem Phys 23:1833-46.
    • (1955) J Chem Phys , vol.23 , pp. 1833-1846
    • Mulliken, R.S.1
  • 92
    • 0033025809 scopus 로고    scopus 로고
    • Predicting binding energetics from structure: looking beyond δG°
    • Murphy KP (1999): Predicting binding energetics from structure: looking beyond δG°. Med Res Rev 19(4):333-9.
    • (1999) Med Res Rev , vol.19 , Issue.4 , pp. 333-339
    • Murphy, K.P.1
  • 94
    • 0031531210 scopus 로고
    • Theoretical aspects of three-dimensional quantitative structureactivity relationships
    • In: Lipkowitz KB, Boyd DB, editors., New York: Wiley-VCH
    • Oprea TI, Waller CL (1991): Theoretical aspects of three-dimensional quantitative structureactivity relationships. In: Lipkowitz KB, Boyd DB, editors. Reviews in Computational Chemistry. New York: Wiley-VCH, pp 127-82.
    • (1991) Reviews in Computational Chemistry , pp. 127-182
    • Oprea, T.I.1    Waller, C.L.2
  • 95
    • 0032698313 scopus 로고    scopus 로고
    • Free energy grids: A practical qualitative application of free energy perturbation to ligand design using the OWFEG method
    • Pearlman DA (1999): Free energy grids: A practical qualitative application of free energy perturbation to ligand design using the OWFEG method. J Med Chem 42:4313-24.
    • (1999) J Med Chem , vol.42 , pp. 4313-4324
    • Pearlman, D.A.1
  • 96
    • 0035865781 scopus 로고    scopus 로고
    • Improved scoring of ligand-protein interactions using OWFEG free energy grids
    • Pearlman DA, Charifson PS (2001): Improved scoring of ligand-protein interactions using OWFEG free energy grids. J Med Chem 44:502-11.
    • (2001) J Med Chem , vol.44 , pp. 502-511
    • Pearlman, D.A.1    Charifson, P.S.2
  • 97
    • 0027166270 scopus 로고
    • Empirical scale of side-chain conformational entropy in protein folding
    • Pickett SD, Sternberg MJE (1993): Empirical scale of side-chain conformational entropy in protein folding. J Mol Biol 231:825-39.
    • (1993) J Mol Biol , vol.231 , pp. 825-839
    • Pickett, S.D.1    Sternberg, M.J.E.2
  • 98
    • 0035966872 scopus 로고    scopus 로고
    • Estimation of binding affinities for selective thrombin inhibitors via Monte Carlo simulations
    • Pierce AC, Jorgensen WL (2001): Estimation of binding affinities for selective thrombin inhibitors via Monte Carlo simulations. J Med Chem 44:1043-50.
    • (2001) J Med Chem , vol.44 , pp. 1043-1050
    • Pierce, A.C.1    Jorgensen, W.L.2
  • 99
    • 0034823225 scopus 로고    scopus 로고
    • The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers
    • Pitera JW, van Gunsteren WF (2001): The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers. J Am Chem Soc 123:3163-4.
    • (2001) J Am Chem Soc , vol.123 , pp. 3163-3164
    • Pitera, J.W.1    van Gunsteren, W.F.2
  • 100
  • 101
    • 0030076041 scopus 로고    scopus 로고
    • Placement of medium-sized molecular fragments into active sites of proteins
    • Rarey M, Wefing S, Lengauer T (1996a) Placement of medium-sized molecular fragments into active sites of proteins. J Comput-Aided Mol Des 10:41-54.
    • (1996) J Comput-Aided Mol Des , vol.10 , pp. 41-54
    • Rarey, M.1    Wefing, S.2    Lengauer, T.3
  • 102
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey M, Kramer B, Lengauer T, Klebe G (1996b) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261:470-89.
    • (1996) J Mol Biol , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 103
    • 0032950520 scopus 로고    scopus 로고
    • Docking of hydrophobic ligands with interaction-based matching algorithms
    • Rarey M, Kramer B, Lengauer T (1999): Docking of hydrophobic ligands with interaction-based matching algorithms. Bioinformatics 15(3):243-50.
    • (1999) Bioinformatics , vol.15 , Issue.3 , pp. 243-250
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3
  • 104
    • 0035905853 scopus 로고    scopus 로고
    • Estimation of binding affinities for HEPT and Nevirapine analogues with HIV-1 reverse transcriptase via Monte Carlo simulations
    • Rizzo RC, Tirado-Rives J, Jorgensen WL (2001): Estimation of binding affinities for HEPT and Nevirapine analogues with HIV-1 reverse transcriptase via Monte Carlo simulations. J Med Chem 44:145-54.
    • (2001) J Med Chem , vol.44 , pp. 145-154
    • Rizzo, R.C.1    Tirado-Rives, J.2    Jorgensen, W.L.3
  • 105
    • 0000763912 scopus 로고
    • Molecular basis for the Born model of ion solvation
    • Roux B, Yu H-A, Karplus M (1990): Molecular basis for the Born model of ion solvation. J Phys Chem 94:4683-8.
    • (1990) J Phys Chem , vol.94 , pp. 4683-4688
    • Roux, B.1    Yu, H.-A.2    Karplus, M.3
  • 106
    • 0032968133 scopus 로고    scopus 로고
    • Implicit solvent models
    • [Review of continuum solvent models and the underlying statistical mechanical basis.]
    • Roux B, Simonson T (1999): Implicit solvent models. Biophys Chem 78:1-20. [Review of continuum solvent models and the underlying statistical mechanical basis.]
    • (1999) Biophys Chem , vol.78 , pp. 1-20
    • Roux, B.1    Simonson, T.2
  • 107
    • 0032572816 scopus 로고    scopus 로고
    • A scoring scheme for discriminating between drugs and nondrugs
    • Sadowski J, Kubinyi H (1998): A scoring scheme for discriminating between drugs and nondrugs. J Med Chem 41:3325-9.
    • (1998) J Med Chem , vol.41 , pp. 3325-3329
    • Sadowski, J.1    Kubinyi, H.2
  • 108
    • 0028940058 scopus 로고
    • An automated computer vision and roboticsbased technique for 3-D flexible biomolecular docking and matching
    • Sandak B, Nussiniov R, Wolfson HJ (1995): An automated computer vision and roboticsbased technique for 3-D flexible biomolecular docking and matching. Comput App Biosci.11:87-99.
    • (1995) Comput App Biosci. , vol.11 , pp. 87-99
    • Sandak, B.1    Nussiniov, R.2    Wolfson, H.J.3
  • 109
    • 0032147007 scopus 로고    scopus 로고
    • Flexible docking allowing induced fit in proteins:Insights from an open to closed conformational isomers
    • Sandak B, Wolfson HJ, Nussinov R (1998): Flexible docking allowing induced fit in proteins:Insights from an open to closed conformational isomers. Proteins 32:159-74.
    • (1998) Proteins , vol.32 , pp. 159-174
    • Sandak, B.1    Wolfson, H.J.2    Nussinov, R.3
  • 110
    • 0031717170 scopus 로고    scopus 로고
    • Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization
    • Schaffer L, Verkhivker GM (1998): Predicting structural effects in HIV-1 protease mutant complexes with flexible ligand docking and protein side-chain optimization. Proteins 33:295-310.
    • (1998) Proteins , vol.33 , pp. 295-310
    • Schaffer, L.1    Verkhivker, G.M.2
  • 111
    • 0033137131 scopus 로고    scopus 로고
    • Prediction of the binding energy for small molecules, peptides and proteins
    • Schapira M, Totrov M, Abagyan R (1999): Prediction of the binding energy for small molecules, peptides and proteins. J Mol Recognit 12:177-90.
    • (1999) J Mol Recognit , vol.12 , pp. 177-190
    • Schapira, M.1    Totrov, M.2    Abagyan, R.3
  • 112
    • 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 98:1978-88.
    • (1994) J Phys Chem , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 113
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still WC, Tempczyk A, Hawley RC, Hendrickson T (1990): Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112:6127-9.
    • (1990) J Am Chem Soc , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hendrickson, T.4
  • 114
    • 0035254959 scopus 로고    scopus 로고
    • Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation
    • Su AI, Lorber DM, Weston GS, Baase WA, Matthews BW, Shoichet BK (2001): Docking molecules by families to increase the diversity of hits in database screens: computational strategy and experimental evaluation. Proteins 42:279-93.
    • (2001) Proteins , vol.42 , pp. 279-293
    • Su, A.I.1    Lorber, D.M.2    Weston, G.S.3    Baase, W.A.4    Matthews, B.W.5    Shoichet, B.K.6
  • 115
  • 116
    • 0032993815 scopus 로고    scopus 로고
    • Scoring functions: a view from the bench
    • Tame JRH (1999): Scoring functions: a view from the bench. J Comput-Aided Mol Des 13:99-108.
    • (1999) J Comput-Aided Mol Des , vol.13 , pp. 99-108
    • Tame, J.R.H.1
  • 117
    • 0031302358 scopus 로고    scopus 로고
    • Flexible protein-ligand docking by global energy optimization in internal coordinates
    • Totrov M, Abagyan R (1997): Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins 29(Suppl. 1):215-20.
    • (1997) Proteins , vol.29 , pp. 215-220
    • Totrov, M.1    Abagyan, R.2
  • 118
    • 0028984540 scopus 로고
    • Protein docking for low-resolution structures
    • Vakser IA (1995): Protein docking for low-resolution structures. Protein Eng 8:371-7.
    • (1995) Protein Eng , vol.8 , pp. 371-377
    • Vakser, I.A.1
  • 119
    • 0035953319 scopus 로고    scopus 로고
    • Property-based design:optimization of drug absorption and pharmacokinetics
    • van de Waterbeemd H, Smith DA, Beaumont K, Walker DK (2001): Property-based design:optimization of drug absorption and pharmacokinetics. J Med Chem 44(9):1313-33.
    • (2001) J Med Chem , vol.44 , Issue.9 , pp. 1313-1333
    • van de Waterbeemd, H.1    Smith, D.A.2    Beaumont, K.3    Walker, D.K.4
  • 120
    • 0028881193 scopus 로고
    • Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity
    • Verkhivker GM, Appelt K, Freer ST, Villafranca JE (1995): Empirical free energy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng 8(7):677-91.
    • (1995) Protein Eng , vol.8 , Issue.7 , pp. 677-691
    • Verkhivker, G.M.1    Appelt, K.2    Freer, S.T.3    Villafranca, J.E.4
  • 122
    • 0000231302 scopus 로고    scopus 로고
    • Assessing energy functions for flexible docking
    • Vieth M, Hirst JD, Kolinski A, Brooks CL, III (1998): Assessing energy functions for flexible docking. J Comp Chem 19(14):1612-22.
    • (1998) J Comp Chem , vol.19 , Issue.14 , pp. 1612-1622
    • Vieth, M.1    Hirst, J.D.2    Kolinski, A.3    Brooks, C.L.4
  • 123
    • 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
    • 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.
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 124
    • 0029119320 scopus 로고
    • A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
    • Wallqvist A, Jernigan RL, Covell DG (1995): A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design. Protein Sci 4:1881-903.
    • (1995) Protein Sci , vol.4 , pp. 1881-1903
    • Wallqvist, A.1    Jernigan, R.L.2    Covell, D.G.3
  • 125
    • 0035978392 scopus 로고    scopus 로고
    • Solvation model based on weighted solvent accessible surface area
    • Wang J, Wang W, Huo S, Lee M, Kollman PA (2001): Solvation model based on weighted solvent accessible surface area. J Phys Chem B 105:5055-67.
    • (2001) J Phys Chem B , vol.105 , pp. 5055-5067
    • Wang, J.1    Wang, W.2    Huo, S.3    Lee, M.4    Kollman, P.A.5
  • 126
    • 0020475509 scopus 로고
    • Calculation of the electric potential in the active site cleft due to α-helix dipoles
    • Warwicker J, Watson HC (1982): Calculation of the electric potential in the active site cleft due to α-helix dipoles. J Mol Biol 157:671-9.
    • (1982) J Mol Biol , vol.157 , pp. 671-679
    • Warwicker, J.1    Watson, H.C.2
  • 127
    • 0034959530 scopus 로고    scopus 로고
    • Large-scale virtual screening for discovering leads in the postgenomic era
    • Waszkowycz B, Perkin TDJ, Sykes RA, Li J (2001): Large-scale virtual screening for discovering leads in the postgenomic era. IBM Sys J 40(2):360-76.
    • (2001) IBM Sys J , vol.40 , Issue.2 , pp. 360-376
    • Waszkowycz, B.1    Perkin, T.D.J.2    Sykes, R.A.3    Li, J.4
  • 128
    • 0030154893 scopus 로고    scopus 로고
    • HAMMERHEAD: fast, fully automated docking of flexible ligands to protein binding sites
    • Welch W, Ruppert J, Jain AN (1996): HAMMERHEAD: fast, fully automated docking of flexible ligands to protein binding sites. Chem Biol 3:449-63.
    • (1996) Chem Biol , vol.3 , pp. 449-463
    • Welch, W.1    Ruppert, J.2    Jain, A.N.3
  • 130
    • 0033081069 scopus 로고    scopus 로고
    • Protein-protein recognition: exploring the energy funnels near the binding sites
    • Zhang C, Chen J, DeLisi C (1999): Protein-protein recognition: exploring the energy funnels near the binding sites. Proteins 34:255-67.
    • (1999) Proteins , vol.34 , pp. 255-267
    • Zhang, C.1    Chen, J.2    DeLisi, C.3
  • 131
    • 0033536456 scopus 로고    scopus 로고
    • Inclusion of solvation in ligand binding free energy calculations using the generalized-Born model
    • Zou X, Sun Y, Kuntz ID (1999): Inclusion of solvation in ligand binding free energy calculations using the generalized-Born model. J Am Chem Soc 121:8033-43.
    • (1999) J Am Chem Soc , vol.121 , pp. 8033-8043
    • Zou, X.1    Sun, Y.2    Kuntz, I.D.3


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