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Volumn 33, Issue 1, 1998, Pages 74-87

Screening a peptidyl database for potential ligands to proteins with side-chain flexibility

Author keywords

Aspartic proteinase; Distance geometry; DNA repair enzyme; Docking; Drug design; Glycosyltransferase; Inducible complementarity; Peptidyl inhibitors; Protein peptide interactions; Serine protease

Indexed keywords

ARTICLE; CONFORMATIONAL TRANSITION; GEOMETRY; HYDROGEN BOND; HYDROPHOBICITY; LIGAND BINDING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; STRUCTURE ANALYSIS;

EID: 0032190489     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19981001)33:1<74::AID-PROT7>3.0.CO;2-L     Document Type: Article
Times cited : (126)

References (62)
  • 1
    • 0023729499 scopus 로고
    • Structural comparison of two serine proteinase-protein inhibitor complexes: Eglin-c-subtilisin Carlsberg and CI-2-subtilisin novo
    • McPhalen, C.A., James, M.N.G. Structural comparison of two serine proteinase-protein inhibitor complexes: Eglin-c-subtilisin Carlsberg and CI-2-subtilisin novo. Biochemistry 27:6582-6598, 1988.
    • (1988) Biochemistry , vol.27 , pp. 6582-6598
    • McPhalen, C.A.1    James, M.N.G.2
  • 2
    • 0029798402 scopus 로고    scopus 로고
    • Functional mimicry of a protein hormone by a peptide agonist: The EPO receptor complex at 2.8 Å
    • Livnah, O., Stura, E.A., Johnson, D.L., Middleton, S.A. et al. Functional mimicry of a protein hormone by a peptide agonist: The EPO receptor complex at 2.8 Å. Science 273:464-471, 1996.
    • (1996) Science , vol.273 , pp. 464-471
    • Livnah, O.1    Stura, E.A.2    Johnson, D.L.3    Middleton, S.A.4
  • 3
    • 0025336463 scopus 로고
    • Emerging approaches in the molecular design of receptor-selective peptide ligands: Conformational, topographical, and dynamic considerations
    • Hruby, V.J., Al-Obeidi, F., Kazmierski, W. Emerging approaches in the molecular design of receptor-selective peptide ligands: Conformational, topographical, and dynamic considerations. Biochem. J. 268:249-262, 1990.
    • (1990) Biochem. J. , vol.268 , pp. 249-262
    • Hruby, V.J.1    Al-Obeidi, F.2    Kazmierski, W.3
  • 4
    • 0028773887 scopus 로고
    • Structure-based drug design: Progress, results and challenges
    • Verlinde, C.L., Hol, W.G. Structure-based drug design: Progress, results and challenges. Structure 2:577-587, 1994.
    • (1994) Structure , vol.2 , pp. 577-587
    • Verlinde, C.L.1    Hol, W.G.2
  • 5
    • 0026730489 scopus 로고
    • Structure-based strategies for drug design and discovery
    • Kuntz, I.D. Structure-based strategies for drug design and discovery. Science 257:1078-1081, 1992.
    • (1992) Science , vol.257 , pp. 1078-1081
    • Kuntz, I.D.1
  • 8
    • 0026345685 scopus 로고
    • Computer design of bioactive molecules: A method for receptor-based de novo ligand design
    • Moon, J.B., Howe, W.J. Computer design of bioactive molecules: A method for receptor-based de novo ligand design. Proteins 11:314-328, 1991.
    • (1991) Proteins , vol.11 , pp. 314-328
    • Moon, J.B.1    Howe, W.J.2
  • 9
    • 0031296607 scopus 로고    scopus 로고
    • Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex
    • Vakser, I.A. Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins Suppl. 1:226-230, 1997.
    • (1997) Proteins Suppl. , vol.1 , pp. 226-230
    • Vakser, I.A.1
  • 10
    • 0000895361 scopus 로고    scopus 로고
    • Peptide docking using dynamic programming
    • Gulukota, K., Vajda, S., DeLisi, C. Peptide docking using dynamic programming. J. Computat. Chem. 17:418-428, 1996.
    • (1996) J. Computat. Chem. , vol.17 , pp. 418-428
    • Gulukota, K.1    Vajda, S.2    DeLisi, C.3
  • 11
    • 0029798563 scopus 로고    scopus 로고
    • Docking enzyme-inhibitor complexes using a preference-based free-energy surface
    • Wallqvist, A., Covell, D.G. Docking enzyme-inhibitor complexes using a preference-based free-energy surface. Proteins 25:403-419, 1996.
    • (1996) Proteins , vol.25 , pp. 403-419
    • Wallqvist, A.1    Covell, D.G.2
  • 12
    • 0029025913 scopus 로고
    • A geometry-based suite of molecular docking processes
    • Fischer, D., Lin, S.L., Wolfson, H.L., Nussinov, R. A geometry-based suite of molecular docking processes. J. Mol. Biol. 248:459-477, 1995.
    • (1995) J. Mol. Biol. , vol.248 , pp. 459-477
    • Fischer, D.1    Lin, S.L.2    Wolfson, H.L.3    Nussinov, R.4
  • 13
    • 0027994352 scopus 로고
    • Predicting molecular interactions and inducible complementarity: Fragment docking of Fab-peptide complexes
    • Friedman, A.R., Roberts, V.A., Tainer, J.A. Predicting molecular interactions and inducible complementarity: Fragment docking of Fab-peptide complexes. Proteins 20: 15-24, 1994.
    • (1994) Proteins , vol.20 , pp. 15-24
    • Friedman, A.R.1    Roberts, V.A.2    Tainer, J.A.3
  • 14
    • 0029294584 scopus 로고
    • Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming
    • Gelhaar, D.K., Verkhivker, G.M., Reijto, P.A. et al. Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: Conformationally flexible docking by evolutionary programming. Chemistry & Biology 2:317-324, 1995.
    • (1995) Chemistry & Biology , vol.2 , pp. 317-324
    • Gelhaar, D.K.1    Verkhivker, G.M.2    Reijto, P.A.3
  • 15
    • 0031581852 scopus 로고    scopus 로고
    • Molecutar docking to ensembles of protein structures
    • Knegtel, R.M.A., Kuntz, I.D., Oshiro, C.M. Molecutar docking to ensembles of protein structures. J. Mol. Biol. 266:424-440, 1997.
    • (1997) J. Mol. Biol. , vol.266 , pp. 424-440
    • Knegtel, R.M.A.1    Kuntz, I.D.2    Oshiro, C.M.3
  • 16
    • 84986467005 scopus 로고
    • Conformational analysis of flexible ligands in macromolecular receptor sites
    • Leach, A.R., Kuntz, I.D. Conformational analysis of flexible ligands in macromolecular receptor sites. J. Computat. Chem. 13:730-748, 1992.
    • (1992) J. Computat. Chem. , vol.13 , pp. 730-748
    • Leach, A.R.1    Kuntz, I.D.2
  • 17
    • 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. 10:41-54, 1996.
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 41-54
    • Rarey, M.1    Wefing, S.2    Lengauer, T.3
  • 18
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey, M., Kramer, B., Lengauer, T., Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 261:470-489, 1996.
    • (1996) J. Mol. Biol. , vol.261 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 19
    • 13344275187 scopus 로고    scopus 로고
    • Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase
    • Strynadka, N.C.J., Eisenstein, M., Katchalski-Katzir, E. et al. Molecular docking programs successfully predict the binding of a β-lactamase inhibitory protein to TEM-1 β-lactamase. Nat. Struct. Biol. 3:233-239, 1996.
    • (1996) Nat. Struct. Biol. , vol.3 , pp. 233-239
    • Strynadka, N.C.J.1    Eisenstein, M.2    Katchalski-Katzir, E.3
  • 20
    • 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. 10:293-304, 1996.
    • (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
  • 21
    • 0028158936 scopus 로고
    • Ligand docking to proteins with discrete side-chain flexibility
    • Leach, A.R. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol. 235:345-356, 1994.
    • (1994) J. Mol. Biol. , vol.235 , pp. 345-356
    • Leach, A.R.1
  • 22
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones, G., Willett, P., Glen, R.C. Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J. Mol. Biol. 245:43-53, 1995.
    • (1995) J. Mol. Biol. , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 23
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • Jones, G., Willett, P., Glen, R.C., Leach, A.R., Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 267:727-748, 1997.
    • (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
  • 25
    • 0027385177 scopus 로고
    • Matching chemistry and shape in molecular docking
    • Shoichet, B.K., Kuntz, I.D. Matching chemistry and shape in molecular docking. Protein Eng. 6:723-732, 1993.
    • (1993) Protein Eng. , vol.6 , pp. 723-732
    • Shoichet, B.K.1    Kuntz, I.D.2
  • 26
    • 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. Chemistry & Biology 3:449-462, 1996.
    • (1996) Chemistry & Biology , vol.3 , pp. 449-462
    • Welch, W.1    Ruppert, J.2    Jain, A.N.3
  • 27
    • 0030979125 scopus 로고    scopus 로고
    • Automatic identification and representation of protein binding sites for molecular docking
    • Ruppert, J., Welch, W., Jain, A.N. Automatic identification and representation of protein binding sites for molecular docking. Protein Sci. 6:524-533, 1997.
    • (1997) Protein Sci. , vol.6 , pp. 524-533
    • Ruppert, J.1    Welch, W.2    Jain, A.N.3
  • 28
    • 33646195474 scopus 로고
    • The hydrogen bond in molecular recognition
    • Fersht, A.R. The hydrogen bond in molecular recognition. Trends in Biochem. Sci. 12:301-304, 1987.
    • (1987) Trends in Biochem. Sci. , vol.12 , pp. 301-304
    • Fersht, A.R.1
  • 29
    • 0025123333 scopus 로고
    • The structure of protein-protein recognition sites
    • Janin, J., Chothia, C. The structure of protein-protein recognition sites. J. Biol. Chem. 265:16027-16030, 1990.
    • (1990) J. Biol. Chem. , vol.265 , pp. 16027-16030
    • Janin, J.1    Chothia, C.2
  • 30
    • 0030598347 scopus 로고    scopus 로고
    • Hydrogen bonding and molecular surface shape complementary as a basis for protein docking
    • Meyer, M., Wilson, P., Schomburg, D. Hydrogen bonding and molecular surface shape complementary as a basis for protein docking. J. Mol. Biol. 264:199-210, 1996.
    • (1996) J. Mol. Biol. , vol.264 , pp. 199-210
    • Meyer, M.1    Wilson, P.2    Schomburg, D.3
  • 31
    • 0027985242 scopus 로고
    • Rational automatic search method for stable docking models of protein and ligand
    • Mizutani, M.Y., Tomioka, N., Itai, A. Rational automatic search method for stable docking models of protein and ligand. J. Mol. Biol. 243:310-326, 1994.
    • (1994) J. Mol. Biol. , vol.243 , pp. 310-326
    • Mizutani, M.Y.1    Tomioka, N.2    Itai, A.3
  • 33
    • 0002192615 scopus 로고
    • A combinatorial algorithm for calculating ligand binding
    • Kuhl, F.S., Crippen, G.M., Friesen, D.K. A combinatorial algorithm for calculating ligand binding. J. Comp. Chem. 5(1):24-34, 1984.
    • (1984) J. Comp. Chem. , vol.5 , Issue.1 , pp. 24-34
    • Kuhl, F.S.1    Crippen, G.M.2    Friesen, D.K.3
  • 34
    • 0026209073 scopus 로고
    • Fast drug-receptor mapping by site-directed distances: A novel method for predicting new pharmacological leads
    • Smellie, A.S., Crippen, G.M., Richards, W.G. Fast drug-receptor mapping by site-directed distances: A novel method for predicting new pharmacological leads. J. Chem. Inf. Comput. Sci. 31:386-392, 1991.
    • (1991) J. Chem. Inf. Comput. Sci. , vol.31 , pp. 386-392
    • Smellie, A.S.1    Crippen, G.M.2    Richards, W.G.3
  • 35
    • 84988128979 scopus 로고
    • Geometrically feasible binding modes of a flexible ligand molecule at the receptor site
    • Ghose, A.K., Crippen, G.M. Geometrically feasible binding modes of a flexible ligand molecule at the receptor site. J. Computat. Chem. 6:350-359, 1985.
    • (1985) J. Computat. Chem. , vol.6 , pp. 350-359
    • Ghose, A.K.1    Crippen, G.M.2
  • 36
    • 0023436445 scopus 로고
    • Designing novel nicotinic agonists by searching a database of molecular shapes
    • Sheridan, R.P., Venkataraghavan, R. Designing novel nicotinic agonists by searching a database of molecular shapes. J. Comput. Aided Mol. Des. 1:243-256, 1987.
    • (1987) J. Comput. Aided Mol. Des. , vol.1 , pp. 243-256
    • Sheridan, R.P.1    Venkataraghavan, R.2
  • 37
    • 0023936327 scopus 로고
    • Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure
    • DesJarlais, R.L., Sheridan, R.P., Seibel, G.L., Dixon, J.S., Kuntz, I.D. Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure. J. Med. Chem. 31:722-729, 1988.
    • (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
  • 38
    • 0026570977 scopus 로고
    • CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure
    • Lawrence, M.C., Davis, P.C. CLIX: A search algorithm for finding novel ligands capable of binding proteins of known three-dimensional structure. Proteins 12:31-41, 1992.
    • (1992) Proteins , vol.12 , pp. 31-41
    • Lawrence, M.C.1    Davis, P.C.2
  • 39
    • 0026209427 scopus 로고
    • An integrated approach to three-dimensional information management with MACCS-3D
    • Gunner, O.F., Hughes, D.W., Dumont, L.M. An integrated approach to three-dimensional information management with MACCS-3D. J. Chem. Inf. Comput. Sci. 31:408-414, 1991.
    • (1991) J. Chem. Inf. Comput. Sci. , vol.31 , pp. 408-414
    • Gunner, O.F.1    Hughes, D.W.2    Dumont, L.M.3
  • 40
    • 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 259:1445-1450, 1993.
    • (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
  • 41
    • 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 29:59-67, 1997.
    • (1997) Proteins , vol.29 , pp. 59-67
    • Gschwend, D.A.1    Sirawaraporn, W.2    Santi, D.V.3    Kuntz, I.D.4
  • 42
    • 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. Computat. Chem. 18(14):1812-1825, 1997.
    • (1997) J. Computat. Chem. , vol.18 , Issue.14 , pp. 1812-1825
    • Makino, S.1    Kuntz, I.D.2
  • 43
    • 0028522983 scopus 로고
    • On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure
    • Böhm, H.-J. On the use of LUDI to search the Fine Chemicals Directory for ligands of proteins of known three-dimensional structure. J. Comput. Aided Mol. Des. 8:623-632, 1994.
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , pp. 623-632
    • Böhm, H.-J.1
  • 44
    • 0026813925 scopus 로고
    • The computer program LUDI: A new method for the de novo design of enzyme inhibitors
    • Böhm, H.-J. The computer program LUDI: A new method for the de novo design of enzyme inhibitors. J. Comput. Aided Mol. Des. 6:61-78, 1992.
    • (1992) J. Comput. Aided Mol. Des. , vol.6 , pp. 61-78
    • Böhm, H.-J.1
  • 45
    • 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. 10:427-440, 1996.
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 427-440
    • Jain, A.N.1
  • 46
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm, U., Sander, C. Enlarged representative set of protein structures. Protein Sci. 3:522-524, 1994.
    • (1994) Protein Sci. , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 48
    • 0029583485 scopus 로고
    • Atomic and residue hydrophilicity in the context of folded protein structures
    • Kuhn, L.A., Swanson, C.A., Pique, M.E., Tainer, J.A., Getzoff, E.D. Atomic and residue hydrophilicity in the context of folded protein structures. Proteins 23:536-547, 1995.
    • (1995) Proteins , vol.23 , pp. 536-547
    • Kuhn, L.A.1    Swanson, C.A.2    Pique, M.E.3    Tainer, J.A.4    Getzoff, E.D.5
  • 49
    • 0030442990 scopus 로고    scopus 로고
    • Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures
    • Hooft, R.W.W., Sander, C., Vriend, G. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins 26:363-376, 1996.
    • (1996) Proteins , vol.26 , pp. 363-376
    • Hooft, R.W.W.1    Sander, C.2    Vriend, G.3
  • 50
    • 0029941271 scopus 로고    scopus 로고
    • Energetics of hydrogen bonding in proteins: A model compound study
    • Habermann, S.M., Murphy, K.P. Energetics of hydrogen bonding in proteins: A model compound study. Protein Sci. 5:1229-1239, 1996.
    • (1996) Protein Sci. , vol.5 , pp. 1229-1239
    • Habermann, S.M.1    Murphy, K.P.2
  • 51
    • 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
    • Böhm, H.-J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput. Aided Mol. Des. 8:243-256, 1994.
    • (1994) J. Comput. Aided Mol. Des. , vol.8 , pp. 243-256
    • Böhm, H.-J.1
  • 52
    • 0029084487 scopus 로고
    • Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: Protein mimicry of DNA
    • Mol, C.D., Arvai, A.S., Sanderson, R.J. et al. Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: Protein mimicry of DNA. Cell 82:701-708, 1995.
    • (1995) Cell , vol.82 , pp. 701-708
    • Mol, C.D.1    Arvai, A.S.2    Sanderson, R.J.3
  • 53
    • 0028934537 scopus 로고
    • Crystal structure and mutational analysis of human uracil-DNA glycosylase: Structural basis for specificity and catalysis
    • Mol, C.D., Arvai, A.S., Slupphaug, G. et al. Crystal structure and mutational analysis of human uracil-DNA glycosylase: Structural basis for specificity and catalysis. Cell 80:869-878, 1995.
    • (1995) Cell , vol.80 , pp. 869-878
    • Mol, C.D.1    Arvai, A.S.2    Slupphaug, G.3
  • 54
    • 3542993893 scopus 로고
    • Structure-based design and two aspartic proteases
    • Lunney, E.A. Structure-based design and two aspartic proteases. Network Science 1:http://www.netsci.org/Science/ Cheminform/feature01.html, 1995.
    • (1995) Network Science , vol.1
    • Lunney, E.A.1
  • 55
    • 0024307344 scopus 로고
    • Three-dimensional structure of cyclodextrin glycosyltransferase from Bacillus circulans at 3.4 Å resolution
    • Hofmann, B.E., Bender, H., Schulz, G.E. Three-dimensional structure of cyclodextrin glycosyltransferase from Bacillus circulans at 3.4 Å resolution. J. Mol. Biol. 209:793-800, 1989.
    • (1989) J. Mol. Biol. , vol.209 , pp. 793-800
    • Hofmann, B.E.1    Bender, H.2    Schulz, G.E.3
  • 56
    • 0026040579 scopus 로고
    • Transplanted LDL and mannose-6-phosphate receptor internalization signals promote high-efficiency endocytosis of the transferrin receptor
    • Collawn, J.F., Kuhn, L.A., Liu, L.-F.S., Tainer, J.A., Trowbridge, I.S. Transplanted LDL and mannose-6-phosphate receptor internalization signals promote high-efficiency endocytosis of the transferrin receptor. EMBO J. 10:3247-3253, 1991.
    • (1991) EMBO J. , vol.10 , pp. 3247-3253
    • Collawn, J.F.1    Kuhn, L.A.2    Liu, L.-F.S.3    Tainer, J.A.4    Trowbridge, I.S.5
  • 57
    • 0032493715 scopus 로고    scopus 로고
    • The role of structure in antibody cross-reactivity between peptides and folded proteins
    • in press
    • Craig, L., Sanschagrin, P.C., Rozek, A., Lackie, S., Kuhn, L.A., Scott, J.K. The role of structure in antibody cross-reactivity between peptides and folded proteins. J. Mol. Biol., 281:in press.
    • J. Mol. Biol. , vol.281
    • Craig, L.1    Sanschagrin, P.C.2    Rozek, A.3    Lackie, S.4    Kuhn, L.A.5    Scott, J.K.6
  • 58
    • 11644261806 scopus 로고    scopus 로고
    • AutoDock 3.0: Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • in press
    • Morris, G.M., Goodsell, D.S., Halliday, R.S. et al. AutoDock 3.0: Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Computat. Chem., in press.
    • J. Computat. Chem.
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3
  • 59
    • 0031592453 scopus 로고    scopus 로고
    • Predicting conserved water-mediated and polar ligand interactions in proteins using a k-nearest-neighbors genetic algorithm
    • Raymer, M.L., Sanschagrin, P.C., Punch, W.F., Venkataraman, S., Goodman, E.D., Kuhn, L.A. Predicting conserved water-mediated and polar ligand interactions in proteins using a k-nearest-neighbors genetic algorithm. J. Mol. Biol. 265:445-464, 1997.
    • (1997) J. Mol. Biol. , vol.265 , pp. 445-464
    • Raymer, M.L.1    Sanschagrin, P.C.2    Punch, W.F.3    Venkataraman, S.4    Goodman, E.D.5    Kuhn, L.A.6
  • 60
    • 0027210349 scopus 로고
    • Principles and pitfalls in designing site-directed peptide ligands
    • Edmundson, A.B., Harris, D.L., Fan, Z.-C. et al. Principles and pitfalls in designing site-directed peptide ligands. Proteins 16:246-267, 1993.
    • (1993) Proteins , vol.16 , pp. 246-267
    • Edmundson, A.B.1    Harris, D.L.2    Fan, Z.-C.3
  • 61
    • 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, M., Kuznetsov, D. ICM-A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. J. Computat. Chem. 15:488-506, 1994.
    • (1994) J. Computat. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 62
    • 0031296786 scopus 로고    scopus 로고
    • Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search
    • Abagyan, R., Batalov, S., Cardozo, T., Totrov, M., Webber, J., Zhou, Y. Homology modeling with internal coordinate mechanics: Deformation zone mapping and improvements of models via conformational search. Proteins Suppl. 1:29-37, 1997.
    • (1997) Proteins Suppl. , vol.1 , pp. 29-37
    • Abagyan, R.1    Batalov, S.2    Cardozo, T.3    Totrov, M.4    Webber, J.5    Zhou, Y.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.