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Volumn 84, Issue 2, 1999, Pages 179-191

Computational approaches to structure-based ligand design

Author keywords

Binding affinity prediction; Computer aided drug design; Database searching; De novo design; Docking; Virtual combinatorial library screening

Indexed keywords

FUNCTIONAL GROUP; LIGAND; PHENOL; THROMBIN INHIBITOR;

EID: 0032828061     PISSN: 01637258     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0163-7258(99)00031-5     Document Type: Review
Times cited : (99)

References (125)
  • 1
    • 0029623184 scopus 로고
    • Computational methods to predict binding free energy in ligand-receptor complexes
    • Ajay M.M.A. Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem. 38:1995;4953-4967.
    • (1995) J Med Chem , vol.38 , pp. 4953-4967
    • Ajay, M.M.A.1
  • 3
    • 0030707764 scopus 로고    scopus 로고
    • Bioinformatics: From genome data to biological knowledge
    • Andrade M.A., Sander C. Bioinformatics. from genome data to biological knowledge Curr Opin Biotechnol. 8:1997;675-683.
    • (1997) Curr Opin Biotechnol , vol.8 , pp. 675-683
    • Andrade, M.A.1    Sander, C.2
  • 4
    • 0028155689 scopus 로고
    • New method for predicting binding-affinity in computer-aided drug design
    • Aqvist J., Medina C., Samuelsson J.E. New method for predicting binding-affinity in computer-aided drug design. Protein Eng. 7:1994;385-391.
    • (1994) Protein Eng , vol.7 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 5
    • 0029894013 scopus 로고    scopus 로고
    • The properties of known drugs. 1. Molecular frameworks
    • Bemis G.W., Murcko M.A. The properties of known drugs. 1. Molecular frameworks. J Med Chem. 39:1996;2887-2893.
    • (1996) J Med Chem , vol.39 , pp. 2887-2893
    • Bemis, G.W.1    Murcko, M.A.2
  • 6
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge D.L., DiCapua F.M. Free energy via molecular simulation. applications to chemical and biomolecular systems Annu Rev Biophys Biophys Chem. 18:1989;431-492.
    • (1989) Annu Rev Biophys Biophys Chem , vol.18 , pp. 431-492
    • Beveridge, D.L.1    Dicapua, F.M.2
  • 7
    • 0028036120 scopus 로고
    • Multiple highly diverse structures complementary to enzyme binding-sites - results of extensive application of a de-novo design method incorporating combinatorial growth
    • Bohacek R.S., McMartin C. Multiple highly diverse structures complementary to enzyme binding-sites - results of extensive application of a de-novo design method incorporating combinatorial growth. J Am Chem Soc. 116:1994;5560-5571.
    • (1994) J Am Chem Soc , vol.116 , pp. 5560-5571
    • Bohacek, R.S.1    McMartin, C.2
  • 8
    • 0001826929 scopus 로고
    • De-novo design of highly diverse structures complementary to enzyme binding-sites - application to thermolysin
    • Bohacek R.S., McMartin C. De-novo design of highly diverse structures complementary to enzyme binding-sites - application to thermolysin. Comput Aided Mol Des. 589:1995;82-97.
    • (1995) Comput Aided Mol des , vol.589 , pp. 82-97
    • Bohacek, R.S.1    McMartin, C.2
  • 9
    • 0027027467 scopus 로고
    • Ludi - rule-based automatic design of new substituents for enzyme-inhibitor leads
    • Bohm H.J. Ludi - rule-based automatic design of new substituents for enzyme-inhibitor leads. J Comput Aided Mol Des. 6:1992;593-606.
    • (1992) J Comput Aided Mol des , vol.6 , pp. 593-606
    • Bohm, H.J.1
  • 10
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known 3-dimensional structure
    • a
    • Bohm H.J. The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known 3-dimensional structure. J Comput Aided Mol Des. 8:1994;243-256. a.
    • (1994) J Comput Aided Mol des , vol.8 , pp. 243-256
    • Bohm, H.J.1
  • 11
    • 0028522983 scopus 로고
    • On the use of Ludi to search the Fine Chemicals Directory for ligands of proteins of known 3-dimensional structure
    • b
    • Bohm H.J. On the use of Ludi to search the Fine Chemicals Directory for ligands of proteins of known 3-dimensional structure. J Comput Aided Mol Des. 8:1994;623-632. b.
    • (1994) J Comput Aided Mol des , vol.8 , pp. 623-632
    • Bohm, H.J.1
  • 12
    • 0030474049 scopus 로고    scopus 로고
    • What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs
    • Bohm H.J., Klebe G. What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs. Angew Chem Int Ed Engl. 35:1996;2588-2614.
    • (1996) Angew Chem Int Ed Engl , vol.35 , pp. 2588-2614
    • Bohm, H.J.1    Klebe, G.2
  • 13
    • 0024566942 scopus 로고
    • New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure
    • Boobbyer D., Goodford P., McWhinnie P., Wade R. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J Med Chem. 32:1989;1083-1094.
    • (1989) J Med Chem , vol.32 , pp. 1083-1094
    • Boobbyer, D.1    Goodford, P.2    McWhinnie, P.3    Wade, R.4
  • 14
    • 0029584358 scopus 로고
    • The meaning of component analysis - decomposition of the free-energy in terms of specific interactions
    • Boresch S., Karplus M. The meaning of component analysis - decomposition of the free-energy in terms of specific interactions. J Mol Biol. 254:1995;801-807.
    • (1995) J Mol Biol , vol.254 , pp. 801-807
    • Boresch, S.1    Karplus, M.2
  • 15
    • 0027968902 scopus 로고
    • Free-energy simulations - The meaning of the individual contributions from a component analysis
    • Boresch S., Archontis G., Karplus M. Free-energy simulations - the meaning of the individual contributions from a component analysis. Proteins. 20:1994;25-33.
    • (1994) Proteins , vol.20 , pp. 25-33
    • Boresch, S.1    Archontis, G.2    Karplus, M.3
  • 16
    • 0002201599 scopus 로고    scopus 로고
    • Combinatorial chemistry
    • Borman S. Combinatorial chemistry. Chem Eng News. 75:1997;43-53.
    • (1997) Chem Eng News , vol.75 , pp. 43-53
    • Borman, S.1
  • 19
    • 0027646168 scopus 로고
    • Workstation clusters rise and shine (Computing in Science: Perspective)
    • Buzbee B. Workstation clusters rise and shine (Computing in Science: Perspective). Science. 261:1993;852-853.
    • (1993) Science , vol.261 , pp. 852-853
    • Buzbee, B.1
  • 20
    • 0030256270 scopus 로고    scopus 로고
    • Computational combinatorial ligand design: Application to human alpha-thrombin
    • Caflisch A. Computational combinatorial ligand design. application to human alpha-thrombin J Comput Aided Mol Des. 10:1996;372-396.
    • (1996) J Comput Aided Mol des , vol.10 , pp. 372-396
    • Caflisch, A.1
  • 21
    • 34249753351 scopus 로고
    • Computational combinatorial chemistry for de novo ligand design: Review and assessment
    • Caflisch A., Karplus M. Computational combinatorial chemistry for de novo ligand design. review and assessment Perspect Drug Discov Des. 3:1995;51-84.
    • (1995) Perspect Drug Discov des , vol.3 , pp. 51-84
    • Caflisch, A.1    Karplus, M.2
  • 22
    • 0027219536 scopus 로고
    • Multiple copy simultaneous search and construction of ligands in binding sites
    • Caflisch A., Miranker A., Karplus M. Multiple copy simultaneous search and construction of ligands in binding sites. J Med Chem. 36:1993;2142-2167.
    • (1993) J Med Chem , vol.36 , pp. 2142-2167
    • Caflisch, A.1    Miranker, A.2    Karplus, M.3
  • 23
    • 0030954877 scopus 로고    scopus 로고
    • Structure-based discovery of ligands targeted to the RNA double helix
    • Chen Q., Shafer R.H., Kuntz I.D. Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry. 36:1997;11402-11407.
    • (1997) Biochemistry , vol.36 , pp. 11402-11407
    • Chen, Q.1    Shafer, R.H.2    Kuntz, I.D.3
  • 24
    • 0030110888 scopus 로고    scopus 로고
    • A technique to study molecular recognition in drug design: Preliminary application of free energy derivatives to inhibition of a malarial cysteine protease
    • Cieplak P., Kollman P.A. A technique to study molecular recognition in drug design. preliminary application of free energy derivatives to inhibition of a malarial cysteine protease J Mol Recognit. 9:1996;103-112.
    • (1996) J Mol Recognit , vol.9 , pp. 103-112
    • Cieplak, P.1    Kollman, P.A.2
  • 28
    • 0032493911 scopus 로고    scopus 로고
    • Supercomputing - computer experts urge new federal initiative
    • Couzin J. Supercomputing - computer experts urge new federal initiative. Science. 281:1998;762.
    • (1998) Science , vol.281 , pp. 762
    • Couzin, J.1
  • 29
    • 0026124585 scopus 로고
    • Electrostatics and diffusion of molecules in solution - simulations with the University-of-Houston-Brownian Dynamics program
    • Davis M.E., Madura J.D., Luty B.A., McCammon J.A. Electrostatics and diffusion of molecules in solution - simulations with the University-of-Houston-Brownian Dynamics program. Comput Phys Commun. 62:1991;187-197.
    • (1991) Comput Phys Commun , vol.62 , pp. 187-197
    • Davis, M.E.1    Madura, J.D.2    Luty, B.A.3    McCammon, J.A.4
  • 30
    • 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 R., Shakhnovich E. Smog. de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence J Am Chem Soc. 118:1996;11733-11744.
    • (1996) J Am Chem Soc , vol.118 , pp. 11733-11744
    • Dewitte, R.1    Shakhnovich, E.2
  • 31
    • 0031003647 scopus 로고    scopus 로고
    • Smog: De novo design method based on simple, fast, and accurate free energy estimates. 2. Case studies on molecular design
    • DeWitte R., Ishchenko A., Shakhnovich E. Smog. de novo design method based on simple, fast, and accurate free energy estimates. 2. Case studies on molecular design J Am Chem Soc. 119:1997;4608-4617.
    • (1997) J Am Chem Soc , vol.119 , pp. 4608-4617
    • Dewitte, R.1    Ishchenko, A.2    Shakhnovich, E.3
  • 32
    • 0030274647 scopus 로고    scopus 로고
    • Genomic sciences and the medicine of tomorrow
    • Drews J. Genomic sciences and the medicine of tomorrow. Nat Biotechnol. 14:1996;1516-1518.
    • (1996) Nat Biotechnol , vol.14 , pp. 1516-1518
    • Drews, J.1
  • 33
    • 0030627637 scopus 로고    scopus 로고
    • Meeting review: The Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996
    • Dunbrack R.L., Gerloff D.L., Bower M., Chen X.W., Lichtarge O., Cohen F.E. Meeting review. The Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996 Fold Des. 2:1997;R27-R42.
    • (1997) Fold des , vol.2
    • Dunbrack, R.L.1    Gerloff, D.L.2    Bower, M.3    Chen, X.W.4    Lichtarge, O.5    Cohen, F.E.6
  • 34
    • 0028282687 scopus 로고
    • Hook: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding sites
    • Eisen M.B., Wiley D.C., Karplus M., Hubbard R.E. Hook. a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding sites Proteins. 19:1994;199-221.
    • (1994) Proteins , vol.19 , pp. 199-221
    • Eisen, M.B.1    Wiley, D.C.2    Karplus, M.3    Hubbard, R.E.4
  • 35
    • 0022596727 scopus 로고
    • Solvation energy in protein folding and binding
    • Eisenberg D., McLachlan A.D. Solvation energy in protein folding and binding. Nature. 319:1986;199-203.
    • (1986) Nature , vol.319 , pp. 199-203
    • Eisenberg, D.1    McLachlan, A.D.2
  • 36
    • 0031226772 scopus 로고    scopus 로고
    • Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    • Eldridge M.D., Murray C.W., Auton T.R., Paolini G.V., Mee R.P. Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des. 11:1997;425-445.
    • (1997) J Comput Aided Mol des , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 39
    • 0345445675 scopus 로고
    • Computer-assisted design of syntheses for heterocyclic-compounds
    • Fick R., Ihlenfeldt W.D., Gasteiger J. Computer-assisted design of syntheses for heterocyclic-compounds. Heterocycles. 40:1995;993-1007.
    • (1995) Heterocycles , vol.40 , pp. 993-1007
    • Fick, R.1    Ihlenfeldt, W.D.2    Gasteiger, J.3
  • 40
    • 0032543623 scopus 로고    scopus 로고
    • Optimizing the binding of fullerene inhibitors of the HIV-1 protease through predicted increases in hydrophobic desolvation
    • Friedman S.H., Ganapathi P.S., Rubin Y., Kenyon G.L. Optimizing the binding of fullerene inhibitors of the HIV-1 protease through predicted increases in hydrophobic desolvation. J Med Chem. 41:1998;2424-2429.
    • (1998) J Med Chem , vol.41 , pp. 2424-2429
    • Friedman, S.H.1    Ganapathi, P.S.2    Rubin, Y.3    Kenyon, G.L.4
  • 41
    • 0031008575 scopus 로고    scopus 로고
    • On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions
    • Froloff N., Windemuth A., Honig B. On the calculation of binding free energies using continuum methods. application to MHC class I protein-peptide interactions Protein Sci. 6:1997;1293-1301.
    • (1997) Protein Sci , vol.6 , pp. 1293-1301
    • Froloff, N.1    Windemuth, A.2    Honig, B.3
  • 42
    • 0024365336 scopus 로고
    • Hidden thermodynamics of mutant proteins - A molecular-dynamics analysis
    • Gao J., Kuczera K., Tidor B., Karplus M. Hidden thermodynamics of mutant proteins - a molecular-dynamics analysis. Science. 244:1989;1069-1072.
    • (1989) Science , vol.244 , pp. 1069-1072
    • Gao, J.1    Kuczera, K.2    Tidor, B.3    Karplus, M.4
  • 43
    • 0027613969 scopus 로고
    • An approximate but efficient method to calculate free-energy trends by computer-simulation - application to dihydrofolate-reductase inhibitor complexes
    • Gerber P.R., Mark A.E., Vangunsteren W.F. An approximate but efficient method to calculate free-energy trends by computer-simulation - application to dihydrofolate-reductase inhibitor complexes. J Comput Aided Mol Des. 7:1993;305-323.
    • (1993) J Comput Aided Mol des , vol.7 , pp. 305-323
    • Gerber, P.R.1    Mark, A.E.2    Vangunsteren, W.F.3
  • 44
    • 0002820943 scopus 로고
    • Sprout, hippo and caesa: Tools for de novo structure generation and estimation of synthetic accessibility
    • Gillet V.J., Myatt G., Zsoldos Z., Johnson A.P. Sprout, hippo and caesa. tools for de novo structure generation and estimation of synthetic accessibility Perspect Drug Discov Des. 3:1995;34-50.
    • (1995) Perspect Drug Discov des , vol.3 , pp. 34-50
    • Gillet, V.J.1    Myatt, G.2    Zsoldos, Z.3    Johnson, A.P.4
  • 45
    • 84988087911 scopus 로고
    • Calculating the electrostatic potential of molecules in solution: Method and error assessment
    • Gilson M.K., Sharp K.A., Honig B.H. Calculating the electrostatic potential of molecules in solution. method and error assessment J Comput Chem. 9:1988;327-335.
    • (1988) J Comput Chem , vol.9 , pp. 327-335
    • Gilson, M.K.1    Sharp, K.A.2    Honig, B.H.3
  • 46
    • 0031058541 scopus 로고    scopus 로고
    • The statistical-thermodynamic basis for computation of binding affinities: A critical review
    • a
    • Gilson M.K., Given J.A., Bush B.L., McCammon J.A. The statistical-thermodynamic basis for computation of binding affinities. a critical review Biophys J. 72:1997;1047-1069. a.
    • (1997) Biophys J , vol.72 , pp. 1047-1069
    • Gilson, M.K.1    Given, J.A.2    Bush, B.L.3    McCammon, J.A.4
  • 47
    • 0031080551 scopus 로고    scopus 로고
    • A new class of models for computing receptor-ligand binding affinities
    • b
    • Gilson M.K., Given J.A., Head M.S. A new class of models for computing receptor-ligand binding affinities. Chem Biol. 4:1997;87-92. b.
    • (1997) Chem Biol , vol.4 , pp. 87-92
    • Gilson, M.K.1    Given, J.A.2    Head, M.S.3
  • 48
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford P. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem. 28:1985;849-857.
    • (1985) J Med Chem , vol.28 , pp. 849-857
    • Goodford, P.1
  • 49
    • 0029705324 scopus 로고    scopus 로고
    • Automated docking of flexible ligands: Applications of AutoDock
    • Goodsell D.S., Morris G.M., Olson A.J. Automated docking of flexible ligands. applications of AutoDock J Mol Recognit. 9:1996;1-5.
    • (1996) J Mol Recognit , vol.9 , pp. 1-5
    • Goodsell, D.S.1    Morris, G.M.2    Olson, A.J.3
  • 50
    • 0030076313 scopus 로고    scopus 로고
    • Functionality map analysis of the active site cleft of human thrombin
    • Grootenhuis P.D.J., Karplus M. Functionality map analysis of the active site cleft of human thrombin. J Comput Aided Mol Des. 10:1996;1-10.
    • (1996) J Comput Aided Mol des , vol.10 , pp. 1-10
    • Grootenhuis, P.D.J.1    Karplus, M.2
  • 51
    • 0001452822 scopus 로고
    • Correlation of binding affinities with nonbonded interaction energies of thrombin-inhibitor complexes
    • Grootenhuis P.D.J., van Galen P.J.M. Correlation of binding affinities with nonbonded interaction energies of thrombin-inhibitor complexes. Acta Crystallogr D. 51:1995;560-566.
    • (1995) Acta Crystallogr D , vol.51 , pp. 560-566
    • Grootenhuis, P.D.J.1    Van Galen, P.J.M.2
  • 52
    • 0003576242 scopus 로고
    • Rational approaches towards protease inhibition: Predicting the binding of thrombin inhibitors
    • G. Wipff. Dordrecht: Kluwer Academic Press
    • Grootenhuis P.D.J., Van Helden S.P. Rational approaches towards protease inhibition. predicting the binding of thrombin inhibitors Wipff G. Computational Approaches in Supramolecular Chemistry. 1994;137-149 Kluwer Academic Press, Dordrecht.
    • (1994) Computational Approaches in Supramolecular Chemistry , pp. 137-149
    • Grootenhuis, P.D.J.1    Van Helden, S.P.2
  • 54
    • 0030964552 scopus 로고    scopus 로고
    • Specificity in structure-based drug design: Identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase
    • Gschwend D.A., Sirawaraporn W., Santi D.V., Kuntz I.D. Specificity in structure-based drug design. Identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase Proteins. 29:1997;59-67.
    • (1997) Proteins , vol.29 , pp. 59-67
    • Gschwend, D.A.1    Sirawaraporn, W.2    Santi, D.V.3    Kuntz, I.D.4
  • 55
    • 0000381173 scopus 로고    scopus 로고
    • Efficient and flexible algorithm for free energy calculations using the lambda-dynamics approach
    • Guo Z., Brooks C.L., Kong X. Efficient and flexible algorithm for free energy calculations using the lambda-dynamics approach. J Phys Chem B. 102:1998;2032-2036.
    • (1998) J Phys Chem B , vol.102 , pp. 2032-2036
    • Guo, Z.1    Brooks, C.L.2    Kong, X.3
  • 56
    • 0037571112 scopus 로고    scopus 로고
    • Merck Molecular Force Field. I. Basis, form, scope, parameterization, and performance of MMFF94
    • Halgren T.A. Merck Molecular Force Field. I. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem. 17:1996;490-519.
    • (1996) J Comput Chem , vol.17 , pp. 490-519
    • Halgren, T.A.1
  • 57
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • Hansson T., Marelius J., Aqvist J. Ligand binding affinity prediction by linear interaction energy methods. J Comput Aided Mol Des. 12:1998;27-35.
    • (1998) J Comput Aided Mol des , vol.12 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Aqvist, J.3
  • 58
    • 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 L.R., Kuntz I.D., White J.M. Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin. irreversible inhibition of infectivity J Virol. 71:1997;8808-8820.
    • (1997) J Virol , vol.71 , pp. 8808-8820
    • Hoffman, L.R.1    Kuntz, I.D.2    White, J.M.3
  • 60
    • 0030666868 scopus 로고    scopus 로고
    • The chemical-biological interface: Developments in automated and miniaturised screening technology
    • Houston J.G., Banks M. The chemical-biological interface. developments in automated and miniaturised screening technology Curr Opin Biotechnol. 8:1997;734-740.
    • (1997) Curr Opin Biotechnol , vol.8 , pp. 734-740
    • Houston, J.G.1    Banks, M.2
  • 61
    • 0030255303 scopus 로고    scopus 로고
    • Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
    • Jain A.N. Scoring noncovalent protein-ligand interactions. a continuous differentiable function tuned to compute binding affinities J Comput Aided Mol Des. 10:1996;427-440.
    • (1996) J Comput Aided Mol des , vol.10 , pp. 427-440
    • Jain, A.N.1
  • 62
    • 0029796290 scopus 로고    scopus 로고
    • Comparison of experimental and computational functional group mapping of an RNase A structure: Implications for computer-aided drug design
    • Joseph-McCarthy D., Fedorov A.A., Almo S.C. Comparison of experimental and computational functional group mapping of an RNase A structure. implications for computer-aided drug design Protein Eng. 9:1996;773-780.
    • (1996) Protein Eng , vol.9 , pp. 773-780
    • Joseph-McCarthy, D.1    Fedorov, A.A.2    Almo, S.C.3
  • 63
    • 0030963674 scopus 로고    scopus 로고
    • Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs
    • Joseph-McCarthy D., Hogle J.M., Karplus M. Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs. Proteins. 29:1997;32-58.
    • (1997) Proteins , vol.29 , pp. 32-58
    • Joseph-McCarthy, D.1    Hogle, J.M.2    Karplus, M.3
  • 64
    • 0031425563 scopus 로고    scopus 로고
    • Bioinformatics in drug discovery
    • Kingsbury D.T. Bioinformatics in drug discovery. Drug Dev Res. 41:1997;120-128.
    • (1997) Drug Dev Res , vol.41 , pp. 120-128
    • Kingsbury, D.T.1
  • 65
    • 7044239742 scopus 로고
    • Free energy calculations: Applications to chemical and biochemical phenomena
    • Kollman P. Free energy calculations. applications to chemical and biochemical phenomena Chem Rev. 93:1993;2395-2417.
    • (1993) Chem Rev , vol.93 , pp. 2395-2417
    • Kollman, P.1
  • 66
    • 0032014733 scopus 로고    scopus 로고
    • Knowledge-based potentials - back to the roots
    • Koppensteiner W.A., Sippl M.J. Knowledge-based potentials - back to the roots. Biochemistry Moscow. 63:1998;247-252.
    • (1998) Biochemistry Moscow , vol.63 , pp. 247-252
    • Koppensteiner, W.A.1    Sippl, M.J.2
  • 67
    • 0031296686 scopus 로고    scopus 로고
    • CASP2 experiences with docking flexible ligands using FLEXX
    • Kramer B., Rarey M., Lengauer T. CASP2 experiences with docking flexible ligands using FLEXX. Proteins (suppl. 1):1997;221-225.
    • (1997) Proteins (Suppl. , vol.1 , pp. 221-225
    • Kramer, B.1    Rarey, M.2    Lengauer, T.3
  • 68
    • 0026730489 scopus 로고
    • Structure-based strategies for drug design and discovery
    • Kuntz I. Structure-based strategies for drug design and discovery. Science. 257:1992;1078-1082.
    • (1992) Science , vol.257 , pp. 1078-1082
    • Kuntz, I.1
  • 70
    • 0028519286 scopus 로고
    • Prediction of new serine proteinase inhibitors
    • Kurinov I.V., Harrison R.W. Prediction of new serine proteinase inhibitors. Nature Struct Biol. 1:1994;735-743.
    • (1994) Nature Struct Biol , vol.1 , pp. 735-743
    • Kurinov, I.V.1    Harrison, R.W.2
  • 71
    • 0028380643 scopus 로고
    • Caveat - A program to facilitate the design of organic-molecules
    • Lauri G., Bartlett P.A. Caveat - a program to facilitate the design of organic-molecules. J Comput Aided Mol Des. 8:1994;51-66.
    • (1994) J Comput Aided Mol des , vol.8 , pp. 51-66
    • Lauri, G.1    Bartlett, P.A.2
  • 72
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T., Karplus M. Effective energy function for proteins in solution. Proteins. 35:1999;133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 75
    • 84986528070 scopus 로고
    • The MM3 force-field for amides, polypeptides and proteins
    • Lii J.H., Allinger N.L. The MM3 force-field for amides, polypeptides and proteins. J Comput Chem. 12:1991;186-199.
    • (1991) J Comput Chem , vol.12 , pp. 186-199
    • Lii, J.H.1    Allinger, N.L.2
  • 76
    • 0030134642 scopus 로고    scopus 로고
    • Estimating the relative free energy of different molecular states with respect to a single reference state
    • Liu H.Y., Mark A.E., vanGunsteren W.F. Estimating the relative free energy of different molecular states with respect to a single reference state. J Phys Chem. 100:1996;9485-9494.
    • (1996) J Phys Chem , vol.100 , pp. 9485-9494
    • Liu, H.Y.1    Mark, A.E.2    Vangunsteren, W.F.3
  • 77
    • 0001349177 scopus 로고    scopus 로고
    • Constructing ab initio force fields for molecular dynamics simulations
    • Liu Y.P., Kim K., Berne B.J., Friesner R.A., Rick S.W. Constructing ab initio force fields for molecular dynamics simulations. J Chem Phys. 108:1998;4739-4755.
    • (1998) J Chem Phys , vol.108 , pp. 4739-4755
    • Liu, Y.P.1    Kim, K.2    Berne, B.J.3    Friesner, R.A.4    Rick, S.W.5
  • 78
    • 0028467094 scopus 로고
    • Computer-assisted synthetic analysis - performance of tactical combinations of transforms
    • Long A.K., Kappos J.C. Computer-assisted synthetic analysis - performance of tactical combinations of transforms. J Chem Inf Comput Sci. 34:1994;915-921.
    • (1994) J Chem Inf Comput Sci , vol.34 , pp. 915-921
    • Long, A.K.1    Kappos, J.C.2
  • 79
    • 0031965676 scopus 로고    scopus 로고
    • Flexible ligand docking using conformational ensembles
    • Lorber D.M., Shoichet B.K. Flexible ligand docking using conformational ensembles. Protein Sci. 7:1998;938-950.
    • (1998) Protein Sci , vol.7 , pp. 938-950
    • Lorber, D.M.1    Shoichet, B.K.2
  • 82
    • 0001139413 scopus 로고    scopus 로고
    • Automated flexible ligand docking method and its application for database search
    • Makino S., Kuntz I.D. Automated flexible ligand docking method and its application for database search. J Comput Chem. 18:1997;1812-1825.
    • (1997) J Comput Chem , vol.18 , pp. 1812-1825
    • Makino, S.1    Kuntz, I.D.2
  • 83
    • 0002496235 scopus 로고    scopus 로고
    • Calculation of ligand binding free energies from molecular dynamics simulations
    • Marelius J., Hansson T., Aqvist J. Calculation of ligand binding free energies from molecular dynamics simulations. Int J Quantum Chem. 69:1998;77-88.
    • (1998) Int J Quantum Chem , vol.69 , pp. 77-88
    • Marelius, J.1    Hansson, T.2    Aqvist, J.3
  • 84
    • 84986525856 scopus 로고
    • A comprehensive study of the rotational energy profiles of organic-systems by ab-initio MO theory, forming a basis for peptide torsional parameters
    • Maxwell D.S., Tiradorives J., Jorgensen W.L. A comprehensive study of the rotational energy profiles of organic-systems by ab-initio MO theory, forming a basis for peptide torsional parameters. J Comput Chem. 16:1995;984-1010.
    • (1995) J Comput Chem , vol.16 , pp. 984-1010
    • Maxwell, D.S.1    Tiradorives, J.2    Jorgensen, W.L.3
  • 85
    • 0031181346 scopus 로고    scopus 로고
    • Qxp: Powerful, rapid computer algorithms for structure-based drug design
    • McMartin C., Bohacek R.S. Qxp. Powerful, rapid computer algorithms for structure-based drug design J Comput Aided Mol Des. 11:1997;333-344.
    • (1997) J Comput Aided Mol des , vol.11 , pp. 333-344
    • McMartin, C.1    Bohacek, R.S.2
  • 86
    • 84986432941 scopus 로고
    • Automated docking with grid-based energy evaluation
    • Meng E.C., Shoichet B.K., Kuntz I.D. Automated docking with grid-based energy evaluation. J Comput Chem. 13:1992;505-524.
    • (1992) J Comput Chem , vol.13 , pp. 505-524
    • Meng, E.C.1    Shoichet, B.K.2    Kuntz, I.D.3
  • 87
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: A multiple copy simultaneous search method
    • Miranker A., Karplus M. Functionality maps of binding sites. a multiple copy simultaneous search method Proteins. 11:1991;29-34.
    • (1991) Proteins , vol.11 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 88
    • 0029586802 scopus 로고
    • An automated method for dynamic ligand design
    • Miranker A., Karplus M. An automated method for dynamic ligand design. Proteins. 23:1995;472-490.
    • (1995) Proteins , vol.23 , pp. 472-490
    • Miranker, A.1    Karplus, M.2
  • 89
    • 0026345685 scopus 로고
    • Computer design of bioactive molecules: A method for receptor-based de novo ligand design
    • Moon J., Howe W. Computer design of bioactive molecules. a method for receptor-based de novo ligand design Proteins. 11:1991;314-328.
    • (1991) Proteins , vol.11 , pp. 314-328
    • Moon, J.1    Howe, W.2
  • 90
    • 0030203710 scopus 로고    scopus 로고
    • Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
    • Morris G.M., Goodsell D.S., Huey R., Olson A.J. Distributed automated docking of flexible ligands to proteins. parallel applications of AutoDock 2.4 J Comput Aided Mol Des. 10:1996;293-304.
    • (1996) J Comput Aided Mol des , vol.10 , pp. 293-304
    • Morris, G.M.1    Goodsell, D.S.2    Huey, R.3    Olson, A.J.4
  • 91
    • 0000036869 scopus 로고    scopus 로고
    • Simulation of activation energies in molecular systems
    • Neria E., Fischer S., Karplus M. Simulation of activation energies in molecular systems. J Chem Phys. 105:1996;1902-1921.
    • (1996) J Chem Phys , vol.105 , pp. 1902-1921
    • Neria, E.1    Fischer, S.2    Karplus, M.3
  • 92
    • 84986486656 scopus 로고
    • A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    • Nicholls A., Honig B. A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comput Chem. 12:1991;435-445.
    • (1991) J Comput Chem , vol.12 , pp. 435-445
    • Nicholls, A.1    Honig, B.2
  • 93
    • 0031547977 scopus 로고    scopus 로고
    • Empirical free energy calculations: A blind test and further improvements to the method
    • Novotny J., Bruccoleri R.E., Davis M., Sharp K.A. Empirical free energy calculations. a blind test and further improvements to the method J Mol Biol. 268:1997;401-411.
    • (1997) J Mol Biol , vol.268 , pp. 401-411
    • Novotny, J.1    Bruccoleri, R.E.2    Davis, M.3    Sharp, K.A.4
  • 95
    • 0023338543 scopus 로고
    • Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
    • Ooi W., Oobataki M., Nemethy G., Scheraga H.A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci USA. 84:1987;3086-3090.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 3086-3090
    • Ooi, W.1    Oobataki, M.2    Nemethy, G.3    Scheraga, H.A.4
  • 96
    • 0009235161 scopus 로고
    • A comparison of alternative approaches to free energy calculations
    • Pearlman D.A. A comparison of alternative approaches to free energy calculations. J Phys Chem. 98:1994;1487-1493.
    • (1994) J Phys Chem , vol.98 , pp. 1487-1493
    • Pearlman, D.A.1
  • 97
    • 0029965861 scopus 로고    scopus 로고
    • Concerts: Dynamic connection of fragments as an approach to de novo ligand design
    • Pearlman D.A., Murcko M. Concerts. dynamic connection of fragments as an approach to de novo ligand design J Med Chem. 39:1996;1651-1663.
    • (1996) J Med Chem , vol.39 , pp. 1651-1663
    • Pearlman, D.A.1    Murcko, M.2
  • 98
    • 0001797110 scopus 로고
    • Rapid generation of high quality approximate 3D molecular structures
    • Pearlman R.S. Rapid generation of high quality approximate 3D molecular structures. Chem Des Aut News. 2:1987;1-6.
    • (1987) Chem des Aut News , vol.2 , pp. 1-6
    • Pearlman, R.S.1
  • 99
    • 0029911948 scopus 로고    scopus 로고
    • For medicinal purposes
    • Petsko G.A. For medicinal purposes. Nature. 384:1996;7-9.
    • (1996) Nature , vol.384 , pp. 7-9
    • Petsko, G.A.1
  • 100
    • 0030076041 scopus 로고    scopus 로고
    • Placement of medium-sized molecular fragments into active sites of proteins
    • Rarey M., Wefing S., Lengauer T. Placement of medium-sized molecular fragments into active sites of proteins. J Comput Aided Mol Des. 10:1996;41-54.
    • (1996) J Comput Aided Mol des , vol.10 , pp. 41-54
    • Rarey, M.1    Wefing, S.2    Lengauer, T.3
  • 101
    • 0027697487 scopus 로고
    • Comparison of conformations of small-molecule structures from the protein data-bank with those generated by Concord, Cobra, Chemdbs-3d, and Converter and those extracted from the Cambridge Structural Database
    • Ricketts E.M., Bradshaw J., Hann M., Hayes F., Tanna N., Ricketts D.M. Comparison of conformations of small-molecule structures from the protein data-bank with those generated by Concord, Cobra, Chemdbs-3d, and Converter and those extracted from the Cambridge Structural Database. J Chem Inf Comput Sci. 33:1993;905-925.
    • (1993) J Chem Inf Comput Sci , vol.33 , pp. 905-925
    • Ricketts, E.M.1    Bradshaw, J.2    Hann, M.3    Hayes, F.4    Tanna, N.5    Ricketts, D.M.6
  • 102
    • 0027480452 scopus 로고
    • Structure-based inhibitor design by using protein models for the development of antiparasitic agents
    • Ring C., Sun E., McKerrow J., Lee G., Rosenthal P., Kuntz I., Cohen F. Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc Natl Acad Sci USA. 90:1993;3583-3587.
    • (1993) Proc Natl Acad Sci USA , vol.90 , pp. 3583-3587
    • Ring, C.1    Sun, E.2    McKerrow, J.3    Lee, G.4    Rosenthal, P.5    Kuntz, I.6    Cohen, F.7
  • 103
    • 0028077638 scopus 로고
    • Structure-assisted design of nonpeptide human immunodeficiency virus-1 protease inhibitors
    • Rose J.R., Craik C.S. Structure-assisted design of nonpeptide human immunodeficiency virus-1 protease inhibitors. Am J Respir Crit Care Med. 150:1994;S176-S182.
    • (1994) Am J Respir Crit Care Med , vol.150
    • Rose, J.R.1    Craik, C.S.2
  • 104
    • 0032521218 scopus 로고    scopus 로고
    • Marrying structure and genomics
    • Rost B. Marrying structure and genomics. Structure. 6:1998;259-263.
    • (1998) Structure , vol.6 , pp. 259-263
    • Rost, B.1
  • 105
  • 106
    • 0027193713 scopus 로고
    • Groupbuild - A fragment-based method for de novo drug design
    • b
    • Rotstein S.H., Murcko M.A. Groupbuild - a fragment-based method for de novo drug design. J Med Chem. 36:1993;1700-1710. b.
    • (1993) J Med Chem , vol.36 , pp. 1700-1710
    • Rotstein, S.H.1    Murcko, M.A.2
  • 107
    • 0025283002 scopus 로고
    • Electrostatic interactions in macromolecules - theory and applications
    • Sharp K.A., Honig B. Electrostatic interactions in macromolecules - theory and applications. Annu Rev Biophys Biophys Chem. 19:1990;301-332.
    • (1990) Annu Rev Biophys Biophys Chem , vol.19 , pp. 301-332
    • Sharp, K.A.1    Honig, B.2
  • 108
    • 0027522358 scopus 로고
    • Structure-based discovery of inhibitors of thymidylate synthase
    • Shoichet B.K., Stroud R.M., Santi D.V., Kuntz I.D., Perry K.M. Structure-based discovery of inhibitors of thymidylate synthase. Science. 259:1993;1445-1450.
    • (1993) Science , vol.259 , pp. 1445-1450
    • Shoichet, B.K.1    Stroud, R.M.2    Santi, D.V.3    Kuntz, I.D.4    Perry, K.M.5
  • 109
    • 0032939345 scopus 로고    scopus 로고
    • Ligand solvation in molecular docking
    • Shoichet B.K., Leach A.R., Kuntz I.D. Ligand solvation in molecular docking. Proteins. 34:1999;4-16.
    • (1999) Proteins , vol.34 , pp. 4-16
    • Shoichet, B.K.1    Leach, A.R.2    Kuntz, I.D.3
  • 110
    • 0029836953 scopus 로고    scopus 로고
    • Discovering high-affinity ligands for proteins: SAR by NMR
    • Shuker S.B., Hajduk P.J., Meadows R.P., Fesik S.W. Discovering high-affinity ligands for proteins. SAR by NMR Science. 274:1996;1531-1534.
    • (1996) Science , vol.274 , pp. 1531-1534
    • Shuker, S.B.1    Hajduk, P.J.2    Meadows, R.P.3    Fesik, S.W.4
  • 111
    • 0031561292 scopus 로고    scopus 로고
    • Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding
    • Simonson T., Archontis G., Karplus M. Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding. J Phys Chem B. 101:1997;8349-8362.
    • (1997) J Phys Chem B , vol.101 , pp. 8349-8362
    • Simonson, T.1    Archontis, G.2    Karplus, M.3
  • 112
    • 0033045557 scopus 로고    scopus 로고
    • A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors
    • So S.S., Karplus M. A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors. J Comput Aided Mol Des. 13:1999;243-258.
    • (1999) J Comput Aided Mol des , vol.13 , pp. 243-258
    • So, S.S.1    Karplus, M.2
  • 113
    • 0005123846 scopus 로고
    • Automated chemical hypothesis generation and database searching with Catalyst®
    • Sprague P.W. Automated chemical hypothesis generation and database searching with Catalyst® Perspect Drug Discov Des. 3:1995;1-20.
    • (1995) Perspect Drug Discov des , vol.3 , pp. 1-20
    • Sprague, P.W.1
  • 115
    • 0345445667 scopus 로고    scopus 로고
    • Pharmacophore-based molecular docking. In O. F. Guner (Ed.), Pharmacophore perception, development, and use in drug design
    • Thomas B.E. IV, Joseph-McCarthy D., Alvarez J.C. Pharmacophore-based molecular docking. In O. F. Guner (Ed.), Pharmacophore perception, development, and use in drug design. La Jolla: International University Press. in press:1999.
    • (1999) La Jolla: International University Press
    • Thomas B.E. IV1    Joseph-McCarthy, D.2    Alvarez, J.C.3
  • 116
    • 33751385859 scopus 로고
    • Simulated annealing on free-energy surfaces by a combined molecular-dynamics and Monte-Carlo approach
    • Tidor B. Simulated annealing on free-energy surfaces by a combined molecular-dynamics and Monte-Carlo approach. J Phys Chem. 97:1993;1069-1073.
    • (1993) J Phys Chem , vol.97 , pp. 1069-1073
    • Tidor, B.1
  • 117
    • 0028773887 scopus 로고
    • Structure-based drug design: Progress, results and challenges
    • Verlinde C.L.M.J., Hol W.G.J. Structure-based drug design. progress, results and challenges Structure. 2:1994;577-587.
    • (1994) Structure , vol.2 , pp. 577-587
    • Verlinde, C.L.M.J.1    Hol, W.G.J.2
  • 118
    • 0030044141 scopus 로고    scopus 로고
    • A study of the active site of influenza virus sialidase: An approach to the rational design of novel anti-influenza drugs
    • von Itzstein M., Dyason J.C., Oliver S.W., White H.F., Wu W.Y., Kok G.B., Pegg M.S. A study of the active site of influenza virus sialidase. an approach to the rational design of novel anti-influenza drugs J Med Chem. 39:1996;388-391.
    • (1996) J Med Chem , vol.39 , pp. 388-391
    • Von Itzstein, M.1    Dyason, J.C.2    Oliver, S.W.3    White, H.F.4    Wu, W.Y.5    Kok, G.B.6    Pegg, M.S.7
  • 119
    • 0027510004 scopus 로고
    • Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds
    • Wade R., Goodford P. Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds. J Med Chem. 36:1993;148-156.
    • (1993) J Med Chem , vol.36 , pp. 148-156
    • Wade, R.1    Goodford, P.2
  • 120
    • 0027439587 scopus 로고
    • Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds
    • Wade R., Clark K., Goodford P. Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds. J Med Chem. 36:1993;140-147.
    • (1993) J Med Chem , vol.36 , pp. 140-147
    • Wade, R.1    Clark, K.2    Goodford, P.3
  • 121
    • 0030154893 scopus 로고    scopus 로고
    • Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
    • Welch W., Ruppert J., Jain A.N. Hammerhead. fast, fully automated docking of flexible ligands to protein binding sites Chem Biol. 3:1996;449-462.
    • (1996) Chem Biol , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.N.3
  • 123
    • 84888116612 scopus 로고    scopus 로고
    • Combinatorial chemistry
    • Wilson E.K. Combinatorial chemistry. Chem Eng News. 75:1997;24-25.
    • (1997) Chem Eng News , vol.75 , pp. 24-25
    • Wilson, E.K.1
  • 124
    • 0031804609 scopus 로고    scopus 로고
    • Inhibitors of HIV-1 protease: A major success of structure-assisted drug design
    • Wlodawer A., Vondrasek J. Inhibitors of HIV-1 protease. a major success of structure-assisted drug design Annu Rev Biophys Biomol Struct. 27:1998;249-284.
    • (1998) Annu Rev Biophys Biomol Struct , vol.27 , pp. 249-284
    • Wlodawer, A.1    Vondrasek, J.2
  • 125
    • 0032540860 scopus 로고    scopus 로고
    • Solution structure and membrane interactions of the C2 domain of cytosolic phospholipase A(2)
    • Xu G.Y., McDonagh T., Yu H.A., Nalefski E.A., Clark J.D., Cumming D.A. Solution structure and membrane interactions of the C2 domain of cytosolic phospholipase A(2). J Mol Biol. 280:1998;485-500.
    • (1998) J Mol Biol , vol.280 , pp. 485-500
    • Xu, G.Y.1    McDonagh, T.2    Yu, H.A.3    Nalefski, E.A.4    Clark, J.D.5    Cumming, D.A.6


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