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Volumn 279, Issue 1, 1998, Pages 287-302

A graph-theoretic algorithm for comparative modeling of protein structure

Author keywords

Clique finding; Comparative modeling; Context sensitivity; Graph theory; Inter connectedness

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPARATIVE STUDY; MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE;

EID: 0032577270     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.1689     Document Type: Article
Times cited : (129)

References (38)
  • 1
    • 0027955787 scopus 로고
    • Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
    • Abagyan R., Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J. Mol. Biol. 235:1994;983-1002
    • (1994) J. Mol. Biol , vol.235 , pp. 983-1002
    • Abagyan, R.1    Totrov, M.2
  • 2
    • 85030336994 scopus 로고
    • Comparison of protein folds and sidechain clusters using algorithms from graph theory
    • Daresbury: SERC, Daresbury Laboratory
    • Artymiuk P., Poirrette A., Rice D., Willett P. Comparison of protein folds and sidechain clusters using algorithms from graph theory. Proceedings of the CCP4 Study Weekend. 1995;SERC, Daresbury Laboratory, Daresbury
    • (1995) Proceedings of the CCP4 Study Weekend
    • Artymiuk, P.1    Poirrette, A.2    Rice, D.3    Willett, P.4
  • 3
    • 0028883794 scopus 로고
    • Determination of the conformation of folding initiation sites in proteins by computer simulation
    • Avbelj F., Moult J. Determination of the conformation of folding initiation sites in proteins by computer simulation. Proteins: Struct. Funct. Genet. 23:1995;129-141
    • (1995) Proteins: Struct. Funct. Genet , vol.23 , pp. 129-141
    • Avbelj, F.1    Moult, J.2
  • 5
    • 0025830469 scopus 로고
    • Method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie J., Lüthy R., Eisenberg D. Method to identify protein sequences that fold into a known three-dimensional structure. Science. 253:1991;164-170
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.1    Lüthy, R.2    Eisenberg, D.3
  • 6
    • 84976668743 scopus 로고
    • Algorithm 457: Finding all cliques of an undirected graph
    • Bron C., Kerbosch J. Algorithm 457 finding all cliques of an undirected graph. Commun. ACM. 16:1973;575-577
    • (1973) Commun. ACM , vol.16 , pp. 575-577
    • Bron, C.1    Kerbosch, J.2
  • 7
    • 84988096360 scopus 로고
    • Monte Carlo simulations for the study of hemoglobin-fragment conformations
    • Chen R. Monte Carlo simulations for the study of hemoglobin-fragment conformations. J. Comput. Chem. 10:1989;488-494
    • (1989) J. Comput. Chem , vol.10 , pp. 488-494
    • Chen, R.1
  • 8
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C., Lesk A. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:1986;823-826
    • (1986) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.2
  • 9
    • 0028786978 scopus 로고
    • The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins
    • Chung S., Subbiah S. The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins. Protein Sci. 4:1995;2300-2309
    • (1995) Protein Sci , vol.4 , pp. 2300-2309
    • Chung, S.1    Subbiah, S.2
  • 10
    • 0028066936 scopus 로고
    • Comparison of systematic search and database methods for constructing segments of protein structure
    • Fidelis K., Stern P., Bacon D., Moult J. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng. 7:1994;953-960
    • (1994) Protein Eng , vol.7 , pp. 953-960
    • Fidelis, K.1    Stern, P.2    Bacon, D.3    Moult, J.4
  • 11
    • 0025287330 scopus 로고
    • Comparative modeling methods: Application to the family of the mammalian serine proteases
    • Greer J. Comparative modeling methods: application to the family of the mammalian serine proteases. Proteins: Struct. Funct. Genet. 7:1990;317-334
    • (1990) Proteins: Struct. Funct. Genet , vol.7 , pp. 317-334
    • Greer, J.1
  • 12
    • 0027511808 scopus 로고
    • Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm
    • Grindley H., Artymiuk P., Rice D., White P. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J. Mol. Biol. 229:1993;707-721
    • (1993) J. Mol. Biol , vol.229 , pp. 707-721
    • Grindley, H.1    Artymiuk, P.2    Rice, D.3    White, P.4
  • 13
    • 0012977835 scopus 로고
    • New York: Garland Publishing Inc
    • Harel D. Algorithmics. 1992;Garland Publishing Inc, New York
    • (1992) Algorithmics
    • Harel, D.1
  • 14
    • 0029844209 scopus 로고    scopus 로고
    • A missing link in cupredoxins: Crystal structure of cucumber stellacyanin at 1.6 Å resolution
    • Hart P., Nersissian A., Herrmann R., Nalbandyan R., Valentine J., Eisenberg D. A missing link in cupredoxins crystal structure of cucumber stellacyanin at 1.6 Å resolution. Protein Sci. 5:1996;2175-2183
    • (1996) Protein Sci , vol.5 , pp. 2175-2183
    • Hart, P.1    Nersissian, A.2    Herrmann, R.3    Nalbandyan, R.4    Valentine, J.5    Eisenberg, D.6
  • 15
    • 0026505184 scopus 로고
    • Evaluation of protein models by atomic solvation preference
    • Holm L., Sander C. Evaluation of protein models by atomic solvation preference. J. Mol. Biol. 225:1992;93-105
    • (1992) J. Mol. Biol , vol.225 , pp. 93-105
    • Holm, L.1    Sander, C.2
  • 16
    • 0031307020 scopus 로고    scopus 로고
    • Competitive assessment of protein fold recognition and threading accuracy
    • Levitt M. Competitive assessment of protein fold recognition and threading accuracy. Proteins: Struct. Funct. Genet. (Sup.1):1997;92-104
    • (1997) Proteins: Struct. Funct. Genet , Issue.SUP.1 , pp. 92-104
    • Levitt, M.1
  • 17
    • 0028774703 scopus 로고
    • Refined structures of the active ser83-cys and impaired ser46-asp histidine-containing phosphocarrier proteins
    • Liao D., Herzberg O. Refined structures of the active ser83-cys and impaired ser46-asp histidine-containing phosphocarrier proteins. Structure. 2:1994;1203-1216
    • (1994) Structure , vol.2 , pp. 1203-1216
    • Liao, D.1    Herzberg, O.2
  • 18
    • 0024310232 scopus 로고
    • Modeling antibody hypervariable loops: A combined algorithm
    • Martin A., Cheetham J., Rees A. Modeling antibody hypervariable loops a combined algorithm. Proc. Natl Acad. Sci. USA. 86:1989;9268-9272
    • (1989) Proc. Natl Acad. Sci. USA , vol.86 , pp. 9268-9272
    • Martin, A.1    Cheetham, J.2    Rees, A.3
  • 20
    • 51249169586 scopus 로고
    • On cliques in graphs
    • Moon J., Moser L. On cliques in graphs. Israel J. Math. 3:1965;23-28
    • (1965) Israel J. Math , vol.3 , pp. 23-28
    • Moon, J.1    Moser, L.2
  • 21
    • 0028864205 scopus 로고
    • A critical assessment of comparative molecular modeling tertiary structures in proteins
    • Mosimann S., Meleshko R., James M. A critical assessment of comparative molecular modeling tertiary structures in proteins. Proteins: Struct. Funct. Genet. 23:1995;301-317
    • (1995) Proteins: Struct. Funct. Genet , vol.23 , pp. 301-317
    • Mosimann, S.1    Meleshko, R.2    James, M.3
  • 23
    • 0025850527 scopus 로고
    • α-Helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease a
    • Okamoto Y., Fukugita M., Nakazawa T., Kawai H. α-Helix folding by Monte Carlo simulated annealing in isolated C-peptide of ribonuclease A. Protein Eng. 4:1991;639-647
    • (1991) Protein Eng , vol.4 , pp. 639-647
    • Okamoto, Y.1    Fukugita, M.2    Nakazawa, T.3    Kawai, H.4
  • 24
    • 0031556019 scopus 로고    scopus 로고
    • Folding simulation with genetic algorithms and a detailed molecular description
    • Pedersen J.T., Moult J. Folding simulation with genetic algorithms and a detailed molecular description. J. Mol. Biol. 269:1997;240-259
    • (1997) J. Mol. Biol , vol.269 , pp. 240-259
    • Pedersen, J.T.1    Moult, J.2
  • 26
    • 0029645286 scopus 로고
    • Structural evidence for the evolutionary divergence of mycoplasma from Gram-positive bacteria: The histidine-containing phosphocarrier protein
    • Pieper U., Kapadia G., Zhu P., Peterkofsky A., Herzberg O. Structural evidence for the evolutionary divergence of mycoplasma from Gram-positive bacteria the histidine-containing phosphocarrier protein. Structure. 3:1995;781-790
    • (1995) Structure , vol.3 , pp. 781-790
    • Pieper, U.1    Kapadia, G.2    Zhu, P.3    Peterkofsky, A.4    Herzberg, O.5
  • 27
    • 0032488962 scopus 로고    scopus 로고
    • An all-atom distance dependent conditional probability discriminatory function for protein structure prediction
    • Samudrala R., Moult J. An all-atom distance dependent conditional probability discriminatory function for protein structure prediction. J. Mol. Biol. 275:1998;893-914
    • (1998) J. Mol. Biol , vol.275 , pp. 893-914
    • Samudrala, R.1    Moult, J.2
  • 28
    • 0031308498 scopus 로고    scopus 로고
    • Handling context-sensitivity in protein structures using graph theory: Bona fide prediction
    • Samudrala R., Moult J. Handling context-sensitivity in protein structures using graph theory: bona fide prediction. Proteins: Struct. Funct. Genet. (Sup.1):1998;43-49
    • (1998) Proteins: Struct. Funct. Genet , Issue.SUP.1 , pp. 43-49
    • Samudrala, R.1    Moult, J.2
  • 29
    • 0028832701 scopus 로고
    • Confronting the problem of interconnected structural changes in the comparative modeling of proteins
    • Samudrala R., Pedersen J., Zhou H., Luo R., Fidelis K., Moult J. Confronting the problem of interconnected structural changes in the comparative modeling of proteins. Proteins: Struct. Funct. Genet. 23:1995;327-336
    • (1995) Proteins: Struct. Funct. Genet , vol.23 , pp. 327-336
    • Samudrala, R.1    Pedersen, J.2    Zhou, H.3    Luo, R.4    Fidelis, K.5    Moult, J.6
  • 31
    • 0029960050 scopus 로고    scopus 로고
    • The hssp database of protein structure-sequence alignments
    • Schneider R., Sander C. The hssp database of protein structure-sequence alignments. Nucl. Acids Res. 24:1996;201-205
    • (1996) Nucl. Acids Res , vol.24 , pp. 201-205
    • Schneider, R.1    Sander, C.2
  • 32
    • 0025608908 scopus 로고
    • Simulations of the folding of a globular protein
    • Skolnick J., Kolinski A. Simulations of the folding of a globular protein. Science. 250:1990;1121-1125
    • (1990) Science , vol.250 , pp. 1121-1125
    • Skolnick, J.1    Kolinski, A.2
  • 33
    • 0027503403 scopus 로고
    • Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms
    • Sun S. Reduced representation model of protein structure prediction statistical potential and genetic algorithms. Protein Sci. 2:1993;762-785
    • (1993) Protein Sci , vol.2 , pp. 762-785
    • Sun, S.1
  • 34
    • 0001513435 scopus 로고
    • Finding a maximum independent set
    • Tarjan R., Trojanowski A. Finding a maximum independent set. SIAM J. Comput. 6:1977;537-546
    • (1977) SIAM J. Comput , vol.6 , pp. 537-546
    • Tarjan, R.1    Trojanowski, A.2
  • 35
    • 0025906759 scopus 로고
    • An analysis of protein folding pathways
    • Unger R., Moult J. An analysis of protein folding pathways. Biochemistry. 30:1991;3816-3823
    • (1991) Biochemistry , vol.30 , pp. 3816-3823
    • Unger, R.1    Moult, J.2
  • 36
    • 0027245418 scopus 로고
    • Genetic algorithms for protein folding simulations
    • Unger R., Moult J. Genetic algorithms for protein folding simulations. J. Mol. Biol. 231:1993;75-81
    • (1993) J. Mol. Biol , vol.231 , pp. 75-81
    • Unger, R.1    Moult, J.2
  • 37
    • 0031301954 scopus 로고    scopus 로고
    • Numerical criteria for evaluating protein structures derived from comparative modeling
    • Venclovas C., Zemla A., Fidelis K., Moult J. Numerical criteria for evaluating protein structures derived from comparative modeling. Proteins: Struct. Funct. Genet. (Sup.1):1997;7-13
    • (1997) Proteins: Struct. Funct. Genet , Issue.SUP.1 , pp. 7-13
    • Venclovas, C.1    Zemla, A.2    Fidelis, K.3    Moult, J.4
  • 38
    • 0025164892 scopus 로고
    • Applications of simulated annealing to peptides
    • Wilson S., Cui W. Applications of simulated annealing to peptides. Biopolymers. 29:1990;225-235
    • (1990) Biopolymers , vol.29 , pp. 225-235
    • Wilson, S.1    Cui, W.2


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