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Volumn 32, Issue , 2003, Pages 335-373

Molecular recognition and docking algorithms

Author keywords

Scoring functions; Search algorithms; Structure based drug design; Thermodynamics of binding; Virtual screening

Indexed keywords

ALGORITHM; DATA BASE; DRUG DEVELOPMENT; HUMAN; MOLECULAR MODEL; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; REVIEW; SCORING SYSTEM; THERMODYNAMICS;

EID: 0042353897     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.32.110601.142532     Document Type: Review
Times cited : (687)

References (149)
  • 1
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan R, Totrov R. 1994. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235:983-1002
    • (1994) J. Mol. Biol. , vol.235 , pp. 983-1002
    • Abagyan, R.1    Totrov, R.2
  • 2
    • 84986522918 scopus 로고
    • ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
    • Abagyan R, Totrov R, Kuznetsov D. 1994. ICM - a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 15:488-506
    • (1994) J. Comput. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, R.2    Kuznetsov, D.3
  • 3
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge Structural Database: A quarter of a million crystal structures and rising
    • Allen FH. 2002. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr. B 58:380-88
    • (2002) Acta Crystallogr. B , vol.58 , pp. 380-388
    • Allen, F.H.1
  • 5
    • 0001382020 scopus 로고    scopus 로고
    • Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions
    • Åqvist J. 1996. Calculation of absolute binding free energies for charged ligands and effects of long-range electrostatic interactions. J. Comput. Chem. 17:1587-97
    • (1996) J. Comput. Chem. , vol.17 , pp. 1587-1597
    • Åqvist, J.1
  • 6
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Åqvist J, Medina C, Samuelsson J-E. 1994. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 7:385-91
    • (1994) Protein Eng. , vol.7 , pp. 385-391
    • Åqvist, J.1    Medina, C.2    Samuelsson, J.-E.3
  • 7
    • 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. 110:741-54
    • (1999) J. Chem. Phys. , vol.110 , 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
  • 8
    • 0033654297 scopus 로고    scopus 로고
    • Generalized Born models of macromolecular solvation effects
    • Bashford D, Case DA. 2000. Generalized Born models of macromolecular solvation effects. Annu. Rev. Phys. Chem. 51:129-52
    • (2000) Annu. Rev. Phys. Chem. , vol.51 , pp. 129-152
    • Bashford, D.1    Case, D.A.2
  • 9
    • 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
  • 10
    • 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
    • Boehm 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. Aid. Mol. Des. 8:243-56
    • (1994) J. Comput. Aid. Mol. Des. , vol.8 , pp. 243-256
    • Boehm, H.-J.1
  • 11
    • 0032112137 scopus 로고    scopus 로고
    • Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
    • Boehm H-J. 1998. Prediction of binding constants of protein ligands: a fast method for the prioritization of hits obtained from de novo design or 3D database search programs. J. Comput. Aid. Mol. Des. 12:309-23
    • (1998) J. Comput. Aid. Mol. Des. , vol.12 , pp. 309-323
    • Boehm, H.-J.1
  • 13
    • 0342645323 scopus 로고    scopus 로고
    • Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection
    • Brown RD, Martin YC. 1996. Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection. J. Chem. Inf. Comput. Sci. 36:572-84
    • (1996) J. Chem. Inf. Comput. Sci. , vol.36 , pp. 572-584
    • Brown, R.D.1    Martin, Y.C.2
  • 14
    • 5244364312 scopus 로고    scopus 로고
    • The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding
    • Brown RD, Martin YC. 1997. The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding. J. Chem. Inf. Comput. Sci. 37:1-9
    • (1997) J. Chem. Inf. Comput. Sci. , vol.37 , pp. 1-9
    • Brown, R.D.1    Martin, Y.C.2
  • 15
    • 0036606101 scopus 로고    scopus 로고
    • Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simlution
    • Buergi R, Kollman PA, van Gunsteren WF. 2002. Simulating proteins at constant pH: an approach combining molecular dynamics and Monte Carlo simlution. Proteins 47:469-80
    • (2002) Proteins , vol.47 , pp. 469-480
    • Buergi, R.1    Kollman, P.A.2    Van Gunsteren, W.F.3
  • 16
    • 0041699615 scopus 로고
    • DOCKER, an interactive program for simulating protein receptor and substrate interactions
    • Busetta B, Tickle IJ, Blundell TL. 1983. DOCKER, an interactive program for simulating protein receptor and substrate interactions. J. Appl. Crystallogr. 16:432-37
    • (1983) J. Appl. Crystallogr. , vol.16 , pp. 432-437
    • Busetta, B.1    Tickle, I.J.2    Blundell, T.L.3
  • 17
    • 0001246354 scopus 로고    scopus 로고
    • Docking by Monte Carlo minimization with a solvation correction: Application to an FKBP-substrate complex
    • Caflisch A, Fischer S, Karplus M. 1997. Docking by Monte Carlo minimization with a solvation correction: application to an FKBP-substrate complex. J. Comput. Chem. 18:723-43
    • (1997) J. Comput. Chem. , vol.18 , pp. 723-743
    • Caflisch, A.1    Fischer, S.2    Karplus, M.3
  • 18
    • 0026721978 scopus 로고
    • Monte Carlo docking of oligopeptides to proteins
    • Caflisch A, Niederer P, Anliker M. 1992. Monte Carlo docking of oligopeptides to proteins. Proteins 13:223-30
    • (1992) Proteins , vol.13 , pp. 223-230
    • Caflisch, A.1    Niederer, P.2    Anliker, M.3
  • 19
    • 33748905333 scopus 로고    scopus 로고
    • Model for aqueous solvation based on class IV atomic charges and first solvation shell effects
    • Chambers CC, Hawkins GD, Cramer DJ, Truhlar DG. 1996. Model for aqueous solvation based on class IV atomic charges and first solvation shell effects. J. Phys. Chem. 100:16385-98
    • (1996) J. Phys. Chem. , vol.100 , pp. 16385-16398
    • Chambers, C.C.1    Hawkins, G.D.2    Cramer, D.J.3    Truhlar, D.G.4
  • 21
    • 0033576680 scopus 로고    scopus 로고
    • Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
    • 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
    • (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
  • 22
    • 0035974484 scopus 로고    scopus 로고
    • Molecular mechanical 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 mechanical 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. Comput. Chem. 22:1048-57
    • (2001) J. Comput. Chem. , vol.22 , pp. 1048-1057
    • Cieplak, P.1    Caldwell, J.W.2    Kollman, P.A.3
  • 24
    • 0035957528 scopus 로고    scopus 로고
    • FlexE: Efficient molecular docking considering protein structure variations
    • Claussen H, Buning C, Rarey M, Lengauer T. 2001. FlexE: efficient molecular docking considering protein structure variations. J. Mol. Biol. 308:377-95
    • (2001) J. Mol. Biol. , vol.308 , pp. 377-395
    • Claussen, H.1    Buning, C.2    Rarey, M.3    Lengauer, T.4
  • 25
    • 0000538815 scopus 로고
    • Analytical molecular surface calculation
    • Connolly ML. 1983. Analytical molecular surface calculation. J. Appl. Crystallogr. 16:548-58
    • (1983) J. Appl. Crystallogr. , vol.16 , pp. 548-558
    • Connolly, M.L.1
  • 26
    • 0025054246 scopus 로고
    • Structure-based design of nonpeptide inhibitors specific for human immunodeficiency virus 1 protease
    • DesJarlais RL, Seibel GL, Kuntz ID, Furth PS, Alvaraz JC, et al. 1990. Structure-based design of nonpeptide inhibitors specific for human immunodeficiency virus 1 protease. Proc. Natl. Acad. Sci. USA 87:6644-48
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 6644-6648
    • DesJarlais, R.L.1    Seibel, G.L.2    Kuntz, I.D.3    Furth, P.S.4    Alvaraz, J.C.5
  • 28
    • 0023936327 scopus 로고
    • Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
    • DesJarlais RL, Sheridan RP, Seibel GL, Dixon JS, Kuntz ID, Venkataraghavan R. 1988. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J. Med. Chem. 31:722-29
    • (1988) J. Med. Chem. , vol.31 , pp. 722-729
    • DesJarlais, R.L.1    Sheridan, R.P.2    Seibel, G.L.3    Dixon, J.S.4    Kuntz, I.D.5    Venkataraghavan, R.6
  • 29
    • 0000934205 scopus 로고    scopus 로고
    • SMoG: De novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence
    • DeWitte RS, Shaknovich EI. 1996. SMoG: de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence. J. Am. Chem. Soc. 118:11733-44
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11733-11744
    • DeWitte, R.S.1    Shaknovich, E.I.2
  • 30
    • 0028291376 scopus 로고
    • Molecular dynamics simulation of the docking of substrates to proteins
    • DiNola A, Roccatano D, Berendsen HJC. 1994. Molecular dynamics simulation of the docking of substrates to proteins. Proteins 19:174-82
    • (1994) Proteins , vol.19 , pp. 174-182
    • DiNola, A.1    Roccatano, D.2    Berendsen, H.J.C.3
  • 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., Jr.2
  • 32
    • 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. Aid. Mol. Des. 15:411-28
    • (2001) J. Comput. Aid. Mol. Des. , vol.15 , pp. 411-428
    • Ewing, T.J.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 33
    • 84892166712 scopus 로고
    • Einfluss der configuration auf die wirkung der enzyme
    • Fischer E. 1894. Einfluss der Configuration auf die wirkung der Enzyme. Ber. 27:2985-93
    • (1894) Ber. , vol.27 , pp. 2985-2993
    • Fischer, E.1
  • 34
    • 0027943261 scopus 로고
    • Conformational isomerism and the diversity of antibodies
    • Foote J, Milstein C. 1994. Conformational isomerism and the diversity of antibodies. Proc. Natl. Acad. Sci. USA 91:10370-74
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 10370-10374
    • Foote, J.1    Milstein, C.2
  • 35
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • Gabb J, 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, J.1    Jackson, R.M.2    Sternberg, M.J.E.3
  • 36
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
    • Gehlhaar DK, Verkhivker GM, Rejto PA, Sherman CJ, Fogel DB, et al. 1995. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. Chem. Biol. 2:317-24
    • (1995) Chem. Biol. , vol.2 , pp. 317-324
    • Gehlhaar, D.K.1    Verkhivker, G.M.2    Rejto, P.A.3    Sherman, C.J.4    Fogel, D.B.5
  • 37
    • 0042200124 scopus 로고    scopus 로고
    • Deleted in proof
    • Deleted in proof
  • 39
    • 0000528756 scopus 로고    scopus 로고
    • The effectiveness of reactant pools for generating structurally-diverse combinatorial libraries
    • Gillet VJ, Willett P, Bradshaw J. 1997. The effectiveness of reactant pools for generating structurally-diverse combinatorial libraries. J. Chem. Inf. Comput. Sci. 37:731-40
    • (1997) J. Chem. Inf. Comput. Sci. , vol.37 , pp. 731-740
    • Gillet, V.J.1    Willett, P.2    Bradshaw, J.3
  • 40
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • Gohlke H, Hendlich M, Klebe G. 2000. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol. 295:337-56
    • (2000) J. Mol. Biol. , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 41
    • 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
  • 42
    • 0025135112 scopus 로고
    • Automated docking of substrates to proteins by simulated annealing
    • Goodsell DS, Olson AJ. 1990. Automated docking of substrates to proteins by simulated annealing. Proteins 8:195-202
    • (1990) Proteins , vol.8 , pp. 195-202
    • Goodsell, D.S.1    Olson, A.J.2
  • 43
    • 0037234043 scopus 로고    scopus 로고
    • Free energy calculations for theophylline binding to an RNA aptamer: Comparison of MM-PBSA and thermodynamic integration methods
    • Gouda H, Kuntz ID, Case DA, Kollman PA. 2002. Free energy calculations for theophylline binding to an RNA aptamer: comparison of MM-PBSA and thermodynamic integration methods. Biopolymers 68:16-34
    • (2002) Biopolymers , vol.68 , pp. 16-34
    • Gouda, H.1    Kuntz, I.D.2    Case, D.A.3    Kollman, P.A.4
  • 44
    • 2442595374 scopus 로고
    • Macromolecular shape and surface maps by solvent exclusion
    • Greer J, Bush BL. 1978. Macromolecular shape and surface maps by solvent exclusion. Proc. Natl. Acad. Sci. USA 75:303-7
    • (1978) Proc. Natl. Acad. Sci. USA , vol.75 , pp. 303-307
    • Greer, J.1    Bush, B.L.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. Aid. Mol. Des. 14:435-48
    • (2000) J. Comput. Aid. Mol. Des. , vol.14 , pp. 435-448
    • Ha, S.1    Andreani, R.2    Robbins, A.3    Muegge, I.4
  • 46
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin I, Ma B, Nussinov R. 2002. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 47:409-43
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Nussinov, R.3
  • 47
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • Hansson T, Marelius J, Åqvist J. 1998. Ligand binding affinity prediction by linear interaction energy methods. J. Comput. Aid. Mol. Des. 12:27-35
    • (1998) J. Comput. Aid. Mol. Des. , vol.12 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Åqvist, J.3
  • 48
    • 0031079364 scopus 로고    scopus 로고
    • "Mining minima": Direct computation of conformational free energy
    • Head MS, Given JA, Gilson MK. 1997. "Mining minima": direct computation of conformational free energy. 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. 120:2710-13
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 2710-2713
    • Helms, V.1    Wade, R.C.2
  • 50
    • 0030753409 scopus 로고    scopus 로고
    • Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: Irreversible inhibition of infectivity
    • Hoffman LR, Kuntz ID, White JM. 1997. Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: irreversible inhibition of infectivity. J. Virol. 71:8808-20
    • (1997) J. Virol. , vol.71 , pp. 8808-8820
    • Hoffman, L.R.1    Kuntz, I.D.2    White, J.M.3
  • 51
    • 0034646180 scopus 로고    scopus 로고
    • Inhibitors of kinesin activity from structure-based computer screening
    • Hopkins SC, Vale RD, Kuntz ID. 2000. Inhibitors of kinesin activity from structure-based computer screening. Biochemistry 39:2805-14
    • (2000) Biochemistry , vol.39 , pp. 2805-2814
    • Hopkins, S.C.1    Vale, R.D.2    Kuntz, I.D.3
  • 52
    • 0037079570 scopus 로고    scopus 로고
    • Computation alanine scanning of the 1:1 human growth hormone-receptor complex
    • Huo S, Massova I, Kollman PA. 2002. Computation alanine scanning of the 1:1 human growth hormone-receptor complex. J. Comput. Chem. 23:15-27
    • (2002) J. Comput. Chem. , vol.23 , pp. 15-27
    • Huo, S.1    Massova, I.2    Kollman, P.A.3
  • 53
    • 0037187412 scopus 로고    scopus 로고
    • Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: Insight into structure-based ligand design
    • Huo S, Wang J, Cieplak P, Kollman PA, Kuntz ID. 2002. Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. J. Med. Chem. 45:1412-19
    • (2002) J. Med. Chem. , vol.45 , pp. 1412-1419
    • Huo, S.1    Wang, J.2    Cieplak, P.3    Kollman, P.A.4    Kuntz, I.D.5
  • 54
    • 0037142298 scopus 로고    scopus 로고
    • SMall Molecule Growth 2001 (SMoG-2001): An improved knowledge-based scoring function for protein-ligand interactions
    • Ishchenko AV, Shaknovich EI. 2002. SMall Molecule Growth 2001 (SMoG-2001): an improved knowledge-based scoring function for protein-ligand interactions. J. Med. Chem. 45:2770-80
    • (2002) J. Med. Chem. , vol.45 , pp. 2770-2780
    • Ishchenko, A.V.1    Shaknovich, E.I.2
  • 55
    • 0032512619 scopus 로고    scopus 로고
    • Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
    • Jackson RM, Gabb HA, Sternberg MJE. 1998. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J. Mol. Biol. 276:265-85
    • (1998) J. Mol. Biol. , vol.276 , pp. 265-285
    • Jackson, R.M.1    Gabb, H.A.2    Sternberg, M.J.E.3
  • 56
    • 0036310711 scopus 로고    scopus 로고
    • On the role of crystal environment in determining protein side-chain conformations
    • Jacobson MP, Friesner RA, Xiang Z, Honig B. 2002. On the role of crystal environment in determining protein side-chain conformations. J. Mol. Biol. 320:597-608
    • (2002) J. Mol. Biol. , vol.320 , pp. 597-608
    • Jacobson, M.P.1    Friesner, R.A.2    Xiang, Z.3    Honig, B.4
  • 57
    • 0033630524 scopus 로고    scopus 로고
    • Evaluation of reagent-based and product-based strategies in the design of combinatorial library subsets
    • Jamois EA, Hassan M, Waldman M. 2000. Evaluation of reagent-based and product-based strategies in the design of combinatorial library subsets. J. Chem. Inf. Comput. Sci. 40:63-70
    • (2000) J. Chem. Inf. Comput. Sci. , vol.40 , pp. 63-70
    • Jamois, E.A.1    Hassan, M.2    Waldman, M.3
  • 58
    • 0036467249 scopus 로고    scopus 로고
    • Potential of mean force for protein-protein interaction studies
    • Jiang F, Gao Y, Mao F, Liu Z, Lai L. 2002. Potential of mean force for protein-protein interaction studies. Proteins 46:190-96
    • (2002) Proteins , vol.46 , pp. 190-196
    • Jiang, F.1    Gao, Y.2    Mao, F.3    Liu, Z.4    Lai, L.5
  • 59
    • 0026310932 scopus 로고
    • "Soft docking": Matching of molecular surface cubes
    • Jiang F, Kim S-H. 1991. "Soft docking": matching of molecular surface cubes. J. Mol. Biol. 219:79-102
    • (1991) J. Mol. Biol. , vol.219 , pp. 79-102
    • Jiang, F.1    Kim, S.-H.2
  • 60
    • 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
  • 61
    • 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
  • 62
    • 0000035913 scopus 로고    scopus 로고
    • Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: Seeking termperatures of maximum density
    • Jorgensen WL, Jenson C. 1998. Temperature dependence of TIP3P, SPC, and TIP4P water from NPT Monte Carlo simulations: seeking termperatures of maximum density. J. Comput. Chem. 19:1179-86
    • (1998) J. Comput. Chem. , vol.19 , pp. 1179-1186
    • Jorgensen, W.L.1    Jenson, C.2
  • 64
    • 0008863560 scopus 로고
    • Some factors in the interpretation of protein denaturation
    • Kauzmann W. 1959. Some factors in the interpretation of protein denaturation. Adv. Protein Chem. 14:1-63
    • (1959) Adv. Protein Chem. , vol.14 , pp. 1-63
    • Kauzmann, W.1
  • 66
    • 0031127997 scopus 로고    scopus 로고
    • Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D
    • Kick EK, Roe DC, Skillman AG, Liu G, Ewing TJA, et al. 1997. Structure-based design and combinatorial chemistry yield low nanomolar inhibitors of cathepsin D. Chem. Biol. 4:297-307
    • (1997) Chem. Biol. , vol.4 , pp. 297-307
    • Kick, E.K.1    Roe, D.C.2    Skillman, A.G.3    Liu, G.4    Ewing, T.J.A.5
  • 67
    • 0033915678 scopus 로고    scopus 로고
    • Recent developments in structure-based drug design
    • Klebe G. 2000. Recent developments in structure-based drug design. J. Mol. Med. 78:269-81
    • (2000) J. Mol. Med. , vol.78 , pp. 269-281
    • Klebe, G.1
  • 68
    • 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. 266:424-40
    • (1997) J. Mol. Biol. , vol.266 , pp. 424-440
    • Knegtel, R.M.A.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 69
    • 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
  • 70
    • 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
  • 71
    • 0034521981 scopus 로고    scopus 로고
    • Calculating structures and free energies of complex molecules: Combining molecular mechanics and continuum models
    • Kollman PA, Massova I, Reyes C, Kuhn B, Huo S, et al. 2000. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33:889-97
    • (2000) Acc. Chem. Res. , vol.33 , pp. 889-897
    • Kollman, P.A.1    Massova, I.2    Reyes, C.3    Kuhn, B.4    Huo, S.5
  • 72
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland DE Jr. 1958. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl. Acad. Sci. USA 44:98-104
    • (1958) Proc. Natl. Acad. Sci. USA , vol.44 , pp. 98-104
    • Koshland D.E., Jr.1
  • 73
    • 0032738842 scopus 로고    scopus 로고
    • Evaluation of the FlexX incremental construction algorithm for protein-ligand docking
    • Kramer B, Rarey M, Lengauer T. 1999. Evaluation of the FlexX incremental construction algorithm for protein-ligand docking. Proteins 37:228-41
    • (1999) Proteins , vol.37 , pp. 228-241
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 74
    • 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. 122:3909-16
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 3909-3916
    • Kuhn, B.1    Kollman, P.A.2
  • 76
    • 0035865951 scopus 로고    scopus 로고
    • Design, docking, and evaluation of multiple libraries against multiple targets
    • Lamb ML, Burdick KW, Toba S, Young MM, Skillman AG, et al. 2001. Design, docking, and evaluation of multiple libraries against multiple targets. Proteins 42:296-88
    • (2001) Proteins , vol.42 , pp. 296-288
    • Lamb, M.L.1    Burdick, K.W.2    Toba, S.3    Young, M.M.4    Skillman, A.G.5
  • 77
    • 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
  • 78
    • 84986467005 scopus 로고
    • Conformational analysis of flexible ligands in macromolecular receptor sights
    • Leach AR, Kuntz ID. 1992. Conformational analysis of flexible ligands in macromolecular receptor sights. J. Comput. Chem. 13:730-48
    • (1992) J. Comput. Chem. , vol.13 , pp. 730-748
    • Leach, A.R.1    Kuntz, I.D.2
  • 79
    • 0035442411 scopus 로고    scopus 로고
    • Direct measurement of protein binding energetics by isothermal titration calorimetry
    • Leavitt S, Freire E. 2001. Direct measurement of protein binding energetics by isothermal titration calorimetry. Curr. Opin. Struct. Biol. 11:560-66
    • (2001) Curr. Opin. Struct. Biol. , vol.11 , pp. 560-566
    • Leavitt, S.1    Freire, E.2
  • 80
    • 0016694062 scopus 로고
    • Hemoglobin interaction in sickle cell fibers. I. Theoretical approaches to the molecular contacts
    • Levinthal C, Wodak SJ, Kahn P, Dadivanian AK. 1975. Hemoglobin interaction in sickle cell fibers. I. Theoretical approaches to the molecular contacts. Proc. Natl. Acad. Sci. USA 72:1330-34
    • (1975) Proc. Natl. Acad. Sci. USA , vol.72 , pp. 1330-1334
    • Levinthal, C.1    Wodak, S.J.2    Kahn, P.3    Dadivanian, A.K.4
  • 81
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li Z, Scheraga HA. 1987. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl. Acad. Sci. USA 84:6611-15
    • (1987) Proc. Natl. Acad. Sci. USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 82
    • 0037157153 scopus 로고    scopus 로고
    • Computational drug design accommodating receptor flexibility: The relaxed complex scheme
    • Lin J-H, Perryman AL, Schames JR, McCammon JA. 2002. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J. Am. Chem. Soc. 124:5632-33
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 5632-5633
    • Lin, J.-H.1    Perryman, A.L.2    Schames, J.R.3    McCammon, J.A.4
  • 83
    • 0034461768 scopus 로고    scopus 로고
    • Drug-like properties and the causes of poor solubility and poor permeability
    • Lipinski CA. 2000. Drug-like properties and the causes of poor solubility and poor permeability. J. Pharmacol. Toxicol. 44:235-49
    • (2000) J. Pharmacol. Toxicol. , vol.44 , pp. 235-249
    • Lipinski, C.A.1
  • 84
    • 0035289779 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. 2001. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 46:3-26
    • (2001) Adv. Drug Deliv. Rev. , vol.46 , pp. 3-26
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 85
    • 0032855301 scopus 로고    scopus 로고
    • MCDOCK: A Monte Carlo simulation approach to the molecular docking problem
    • Liu M, Wang S. 1999. MCDOCK: a Monte Carlo simulation approach to the molecular docking problem. J. Comput. Aid. Mol. Des. 13:435-51
    • (1999) J. Comput. Aid. Mol. Des. , vol.13 , pp. 435-451
    • Liu, M.1    Wang, S.2
  • 86
    • 0031965676 scopus 로고    scopus 로고
    • Flexible ligand docking using conformational ensembles
    • Lorber DM, Shoichet BK. 1998. Flexible ligand docking using conformational ensembles. Protein Sci. 7:938-50
    • (1998) Protein Sci. , vol.7 , pp. 938-950
    • Lorber, D.M.1    Shoichet, B.K.2
  • 87
    • 0035155532 scopus 로고    scopus 로고
    • Diffusion constant of the TIP5P model of liquid water
    • Mahoney MW, Jorgensen WL. 2001. Diffusion constant of the TIP5P model of liquid water. J. Chem. Phys. 114:363-66
    • (2001) J. Chem. Phys. , vol.114 , pp. 363-366
    • Mahoney, M.W.1    Jorgensen, W.L.2
  • 88
    • 0033135477 scopus 로고    scopus 로고
    • Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation
    • Mangoni M, Roccatano D, Di Nola A. 1999. Docking of flexible ligands to flexible receptors in solution by molecular dynamics simulation. Proteins 35:153-62
    • (1999) Proteins , vol.35 , pp. 153-162
    • Mangoni, M.1    Roccatano, D.2    Di Nola, A.3
  • 89
    • 0002496235 scopus 로고    scopus 로고
    • Calculation of ligand binding free energies from molecular dynamics simulations
    • Marelius J, Hansson T, Åqvist J. 1998. Calculation of ligand binding free energies from molecular dynamics simulations. Int. J. Quantum Chem. 69:77-88
    • (1998) Int. J. Quantum Chem. , vol.69 , pp. 77-88
    • Marelius, J.1    Hansson, T.2    Åqvist, J.3
  • 90
    • 0037068532 scopus 로고    scopus 로고
    • Do structurally similar molecules have similar biological activity?
    • Martin YC, Kofron JL, Traphagen LM. 2002. Do structurally similar molecules have similar biological activity? J. Med. Chem. 45:4350-58
    • (2002) J. Med. Chem. , vol.45 , pp. 4350-4358
    • Martin, Y.C.1    Kofron, J.L.2    Traphagen, L.M.3
  • 91
    • 0033568644 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • 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. 121:8133-43
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 92
    • 0001127721 scopus 로고    scopus 로고
    • Free energies of solvation in chloroform and water from a linear response approach
    • McDonald NA, Carlson HA, Jorgensen WL. 1997. Free energies of solvation in chloroform and water from a linear response approach. J. Phys. Org. Chem. 10:563-76
    • (1997) J. Phys. Org. Chem. , vol.10 , pp. 563-576
    • McDonald, N.A.1    Carlson, H.A.2    Jorgensen, W.L.3
  • 94
    • 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
  • 95
    • 0028412035 scopus 로고
    • FLOG: A system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure
    • Miller MD, Kearsley SK, Underwood DJ, Sheridan RP. 1994. FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure. J. Comput. Aid. Mol. Des. 8:153-74
    • (1994) J. Comput. Aid. Mol. Des. , vol.8 , pp. 153-174
    • Miller, M.D.1    Kearsley, S.K.2    Underwood, D.J.3    Sheridan, R.P.4
  • 96
    • 0000823044 scopus 로고    scopus 로고
    • BLEEP - Potential of mean force describing protein-ligand interactions. I. Generating potential
    • Mitchell JBO, Laskowski RA, Alex A, Thornton JM. 1999. BLEEP - potential of mean force describing protein-ligand interactions. I. Generating potential. J. Comput. Chem. 20:1165-76
    • (1999) J. Comput. Chem. , vol.20 , pp. 1165-1176
    • Mitchell, J.B.O.1    Laskowski, R.A.2    Alex, A.3    Thornton, J.M.4
  • 97
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical free energy function
    • Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, et al. 1998. Automated docking using a Lamarckian genetic algorithm and an empirical free energy function. J. Comput. Chem. 19:1639-62
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5
  • 98
    • 0033545622 scopus 로고    scopus 로고
    • A general and fast scoring function for protein-ligand interactions: A simplified potential approach
    • Muegge I, Martin YC. 1999. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 42:791-804
    • (1999) J. Med. Chem. , vol.42 , pp. 791-804
    • Muegge, I.1    Martin, Y.C.2
  • 99
    • 0032718788 scopus 로고    scopus 로고
    • The sensitivity of the results of molecular docking to induced effects: Application to thrombin, thermolysin and neuraminidase
    • Murray CW, Baxter CA, Frenkel AD. 1999. The sensitivity of the results of molecular docking to induced effects: application to thrombin, thermolysin and neuraminidase. J. Comput. Aid. Mol. Des. 13:547-62
    • (1999) J. Comput. Aid. Mol. Des. , vol.13 , pp. 547-562
    • Murray, C.W.1    Baxter, C.A.2    Frenkel, A.D.3
  • 100
    • 0043202470 scopus 로고    scopus 로고
    • Deleted in proof
    • Deleted in proof
  • 101
    • 0031592919 scopus 로고    scopus 로고
    • Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation
    • Nakajima N, Higo J, Kidera A, Nakamura H. 1997. Flexible docking of a ligand peptide to a receptor protein by multicanonical molecular dynamics simulation. Chem. Phys. 278:297-301
    • (1997) Chem. Phys. , vol.278 , pp. 297-301
    • Nakajima, N.1    Higo, J.2    Kidera, A.3    Nakamura, H.4
  • 102
    • 0030819348 scopus 로고    scopus 로고
    • Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides
    • Nakajima N, Nakamura H, Kidera A. 1997. Multicanonical ensemble generated by molecular dynamics simulation for enhanced conformational sampling of peptides. J. Phys. Chem. B 101:817-24
    • (1997) J. Phys. Chem. B , vol.101 , pp. 817-824
    • Nakajima, N.1    Nakamura, H.2    Kidera, A.3
  • 103
    • 84986486656 scopus 로고
    • A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • Nicholls A, Honig B. 1991. A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comput. Chem. 12:435-45
    • (1991) J. Comput. Chem. , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 104
  • 105
    • 0037110472 scopus 로고    scopus 로고
    • Effective Born radii in the generalized Born approximation: The importance of being perfect
    • Onufriev A, Case DA, Bashford D. 2002. Effective Born radii in the generalized Born approximation: the importance of being perfect. J. Comput. Chem. 23:1297-304
    • (2002) J. Comput. Chem. , vol.23 , pp. 1297-1304
    • Onufriev, A.1    Case, D.A.2    Bashford, D.3
  • 106
    • 0036589285 scopus 로고    scopus 로고
    • Current trends in lead discovery: Are we looking for the appropriate properties?
    • Oprea TI. 2002. Current trends in lead discovery: Are we looking for the appropriate properties? J. Comput. Aid. Mol. Des. 16:325-34
    • (2002) J. Comput. Aid. Mol. Des. , vol.16 , pp. 325-334
    • Oprea, T.I.1
  • 108
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
    • Osterberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS. 2002. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 46:34-40
    • (2002) Proteins , vol.46 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 109
    • 0000302276 scopus 로고    scopus 로고
    • Application of a molecular dynamics simulation method with a generalized effective potential to the flexible molecular docking problems
    • Pak Y, Wang S. 2000. Application of a molecular dynamics simulation method with a generalized effective potential to the flexible molecular docking problems. J. Phys. Chem. B 104:354-59
    • (2000) J. Phys. Chem. B , vol.104 , pp. 354-359
    • Pak, Y.1    Wang, S.2
  • 110
    • 0035976367 scopus 로고    scopus 로고
    • EUDOC: A computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases
    • Pang Y-P, Perola E, Xu K, Prendergast FG. 2001. EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases. J. Comput. Chem. 22:1750-71
    • (2001) J. Comput. Chem. , vol.22 , pp. 1750-1771
    • Pang, Y.-P.1    Perola, E.2    Xu, K.3    Prendergast, F.G.4
  • 111
    • 84988103815 scopus 로고
    • Computer graphics in real-time docking with energy calculation and minimization
    • Pattabiraman N, Levitt M, Ferrin TE, Langridge R. 1985. Computer graphics in real-time docking with energy calculation and minimization. J. Comput. Chem. 6:432-36
    • (1985) J. Comput. Chem. , vol.6 , pp. 432-436
    • Pattabiraman, N.1    Levitt, M.2    Ferrin, T.E.3    Langridge, R.4
  • 112
    • 0001971367 scopus 로고
    • The nature of the intermolecular forces operative in biological processes
    • Pauling L, Delbrück M. 1940. The nature of the intermolecular forces operative in biological processes. Science 92:77-79
    • (1940) Science , vol.92 , pp. 77-79
    • Pauling, L.1    Delbrück, M.2
  • 113
    • 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
  • 114
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey M, Kramer B, Lengauer T, Klebe G. 1996. 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
  • 115
    • 0030076041 scopus 로고    scopus 로고
    • Placement of medium-sized molecular fragments into active sites of proteins
    • Rarey M, Wefing S, Lengauer T. 1996. Placement of medium-sized molecular fragments into active sites of proteins. J. Comput. Aid. Mol. Des. 10:41-54
    • (1996) J. Comput. Aid. Mol. Des. , vol.10 , pp. 41-54
    • Rarey, M.1    Wefing, S.2    Lengauer, T.3
  • 116
    • 26844574873 scopus 로고
    • Hydration phenomena, classical electrostatics and the boundary element method
    • Rashin AA. 1990. Hydration phenomena, classical electrostatics and the boundary element method. J. Phys. Chem. 94:1725-33
    • (1990) J. Phys. Chem. , vol.94 , pp. 1725-1733
    • Rashin, A.A.1
  • 117
    • 0034614387 scopus 로고    scopus 로고
    • Investigating the binding specificity of U1A-RNA by computational mutagenesis
    • Reyes C, Kollman PA. 2000. Investigating the binding specificity of U1A-RNA by computational mutagenesis. J. Mol. Biol. 295:1-6
    • (2000) J. Mol. Biol. , vol.295 , pp. 1-6
    • Reyes, C.1    Kollman, P.A.2
  • 118
    • 0017429069 scopus 로고
    • Areas, volumes, packing, and protein structure
    • Richards FM. 1977. Areas, volumes, packing, and protein structure. Annu. Rev. Biophys. Bioeng. 6:151-76
    • (1977) Annu. Rev. Biophys. Bioeng. , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 119
    • 0034722975 scopus 로고    scopus 로고
    • Validation of a model for the complex of HIV-1 reverse transcriptase with sustiva through computation of resistance profiles
    • Rizzo RC, Wang D-P, Tirado-Rives J, Jorgensen WL. 2000. Validation of a model for the complex of HIV-1 reverse transcriptase with sustiva through computation of resistance profiles. J. Am. Chem. Soc. 122:12898-900
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 12898-12900
    • Rizzo, R.C.1    Wang, D.-P.2    Tirado-Rives, J.3    Jorgensen, W.L.4
  • 121
    • 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
  • 122
    • 0034092711 scopus 로고    scopus 로고
    • Analysis of knowledge-based protein-ligand potentials using a self-consistent method
    • Shimada J, Ishchenko AV, Shaknovich EI. 2000. Analysis of knowledge-based protein-ligand potentials using a self-consistent method. Protein Sci. 9:765-75
    • (2000) Protein Sci. , vol.9 , pp. 765-775
    • Shimada, J.1    Ishchenko, A.V.2    Shaknovich, E.I.3
  • 124
    • 0043202469 scopus 로고    scopus 로고
    • Deleted in proof
    • Deleted in proof
  • 125
    • 20644437755 scopus 로고    scopus 로고
    • Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method
    • Smith RH Jr, Jorgensen WL, Tirado-Rives J, Lamb ML, Janssen PAJ, et al. 1998. Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method. J. Med. Chem. 41:5272-86
    • (1998) J. Med. Chem. , vol.41 , pp. 5272-5286
    • Smith R.H., Jr.1    Jorgensen, W.L.2    Tirado-Rives, J.3    Lamb, M.L.4    Janssen, P.A.J.5
  • 126
    • 0037038372 scopus 로고    scopus 로고
    • Absolute comparison of simulated and experimental protein-folding dynamics
    • Snow CD, Nguyen H, Pande VS, Gruebele M. 2002. Absolute comparison of simulated and experimental protein-folding dynamics. Nature 420:102-6
    • (2002) Nature , vol.420 , pp. 102-106
    • Snow, C.D.1    Nguyen, H.2    Pande, V.S.3    Gruebele, M.4
  • 128
    • 0035966871 scopus 로고    scopus 로고
    • Detailed analysis of scoring functions for virtual screening
    • Stahl M, Rarey M. 2001. Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 44:1035-42
    • (2001) J. Med. Chem. , vol.44 , pp. 1035-1042
    • Stahl, M.1    Rarey, M.2
  • 129
    • 0344778061 scopus 로고
    • Semianalytical treatment of solvation for molecular mechanics and dynamics
    • Still WC, Tempczyk A, Hawley RC, Hedrickson T. 1990. Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc. 112:6127-29
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 6127-6129
    • Still, W.C.1    Tempczyk, A.2    Hawley, R.C.3    Hedrickson, T.4
  • 130
    • 0023438480 scopus 로고
    • A method for fast energy estimation and visualization of protein-ligand interaction
    • Tomioka N, Itai A, Iitaka Y. 1987. A method for fast energy estimation and visualization of protein-ligand interaction. J. Comput. Aid. Mol. Des. 1:197-210
    • (1987) J. Comput. Aid. Mol. Des. , vol.1 , pp. 197-210
    • Tomioka, N.1    Itai, A.2    Iitaka, Y.3
  • 131
    • 0031302358 scopus 로고    scopus 로고
    • Flexible protein-ligand docking by global energy optimization in internal coordinates
    • Totrov R, Abagyan R. 1997. Flexible protein-ligand docking by global energy optimization in internal coordinates. Proteins (Suppl.) 1:215-20
    • (1997) Proteins (Suppl.) , vol.1 , pp. 215-220
    • Totrov, R.1    Abagyan, R.2
  • 132
    • 0032493375 scopus 로고    scopus 로고
    • Reaching the global minimum in docking simulations: A Monte Carlo energy minimization approach using Bezier Splines
    • Trosset J-Y, Scheraga HA. 1998. Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier Splines. Proc. Natl. Acad. Sci. USA 95:8011-15
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 8011-8015
    • Trosset, J.-Y.1    Scheraga, H.A.2
  • 133
    • 0345483185 scopus 로고    scopus 로고
    • Prodock: Software package for protein modeling and docking
    • Trosset J-Y, Scheraga HA. 1999. Prodock: software package for protein modeling and docking. J. Comput. Chem. 20:412-27
    • (1999) J. Comput. Chem. , vol.20 , pp. 412-427
    • Trosset, J.-Y.1    Scheraga, H.A.2
  • 137
    • 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 explicit solvent and a continuum solvent models
    • 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 explicit solvent and a continuum solvent models. Proteins 32:399-413
    • (1998) Proteins , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 139
    • 0033168443 scopus 로고    scopus 로고
    • Flexible ligand docking: A multistep strategy approach
    • Wang J, Kollman PA, Kuntz ID. 1999. Flexible ligand docking: a multistep strategy approach. Proteins 36:1-19
    • (1999) Proteins , vol.36 , pp. 1-19
    • Wang, J.1    Kollman, P.A.2    Kuntz, I.D.3
  • 140
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in reproducing the binding free energies of HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of Efivirenz by docking and MM-PBSA
    • Wang J, Morin P, Wang W, Kollman PA. 2001. Use of MM-PBSA in reproducing the binding free energies of HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of Efivirenz by docking and MM-PBSA. J. Am. Chem. Soc. 123:5221-30
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 5221-5230
    • Wang, J.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 141
    • 0035978392 scopus 로고    scopus 로고
    • Solvation model based on weighted solvent accessible surface area
    • Wang J, Wang W, Huo S, Lee MR, 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.R.4    Kollman, P.A.5
  • 142
    • 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. 3:449-62
    • (1996) Chem. Biol. , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.N.3
  • 143
    • 0029933286 scopus 로고    scopus 로고
    • Prediction of protein complexes using empirical free energy functions
    • Weng Z, Vajda S, DeLisi C. 1996. Prediction of protein complexes using empirical free energy functions. Protein Sci. 5:614-26
    • (1996) Protein Sci. , vol.5 , pp. 614-626
    • Weng, Z.1    Vajda, S.2    DeLisi, C.3
  • 144
    • 0031135364 scopus 로고    scopus 로고
    • A comparison of heuristic search algorithms for molecular docking
    • Westhead DR, Clark DE, Murray CW. 1997. A comparison of heuristic search algorithms for molecular docking. J. Comput. Aid. Mol. Des. 11:209-28
    • (1997) J. Comput. Aid. Mol. Des. , vol.11 , pp. 209-228
    • Westhead, D.R.1    Clark, D.E.2    Murray, C.W.3
  • 146
    • 0018165127 scopus 로고
    • Computer analysis of protein-protein interactions
    • Wodak SJ, Janin J. 1978. Computer analysis of protein-protein interactions. J. Mol. Biol. 124:323-42
    • (1978) J. Mol. Biol. , vol.124 , pp. 323-342
    • Wodak, S.J.1    Janin, J.2
  • 147
    • 0036234027 scopus 로고    scopus 로고
    • Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water
    • Xia B, Tsui V, Case DA, Dyson HJ, Wright PE. 2002. Comparison of protein solution structures refined by molecular dynamics simulation in vacuum, with a generalized Born model, and with explicit water. J. Biomol. NMR 22:317-31
    • (2002) J. Biomol. NMR , vol.22 , pp. 317-331
    • Xia, B.1    Tsui, V.2    Case, D.A.3    Dyson, H.J.4    Wright, P.E.5
  • 148
    • 0035950792 scopus 로고    scopus 로고
    • New linear interaction method for binding affinity calculations using a continuum solvent model
    • Zhou R, Friesner RA, Ghosh A, Rizzo RC, Jorgensen WL, Levy RM. 2001. New linear interaction method for binding affinity calculations using a continuum solvent model. J. Phys. Chem. B 105:10388-97
    • (2001) J. Phys. Chem. B , vol.105 , pp. 10388-10397
    • Zhou, R.1    Friesner, R.A.2    Ghosh, A.3    Rizzo, R.C.4    Jorgensen, W.L.5    Levy, R.M.6
  • 149
    • 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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