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Volumn 11, Issue 6, 2004, Pages 1061-1072

PROuST: A comparison method of three-dimensional structures of proteins using indexing techniques

Author keywords

Dynamic programming; Indexing; Protein structure comparison; Secondary structure

Indexed keywords

PROTEIN;

EID: 12844261137     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2004.11.1061     Document Type: Article
Times cited : (25)

References (31)
  • 1
    • 0024677985 scopus 로고
    • An automatic search for similar spatial arrangements of α helices and β-strands in globular proteins
    • Abagyan, R.A., and Maiorov, V.N. 1989. An automatic search for similar spatial arrangements of α helices and β-strands in globular proteins. J. Mol. Struct. Dyn. 6(5), 1045-1060.
    • (1989) J. Mol. Struct. Dyn. , vol.6 , Issue.5 , pp. 1045-1060
    • Abagyan, R.A.1    Maiorov, V.N.2
  • 2
    • 0030377824 scopus 로고    scopus 로고
    • Protein structure alignment using dynamic programming and iterative improvement
    • Akutsu, T. 1996. Protein structure alignment using dynamic programming and iterative improvement. IEICE Trans. Inf. Syst. E78-D, 0, 1-8.
    • (1996) IEICE Trans. Inf. Syst. , vol.E78-D , pp. 1-8
    • Akutsu, T.1
  • 3
    • 0030464952 scopus 로고    scopus 로고
    • Detection of non-topological motifs in protein structures
    • Alesker, A., Nussinov, R., and Wolfson, H.J. 1996. Detection of non-topological motifs in protein structures. Protein Eng. 9(5), 1103-1119.
    • (1996) Protein Eng. , vol.9 , Issue.5 , pp. 1103-1119
    • Alesker, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 6
    • 0001547102 scopus 로고    scopus 로고
    • A protein structure comparison methodology
    • Brown, N.P., Orengo, C.A., and Taylor, W.R. 1996. A protein structure comparison methodology. Comp. Chem. 27, 359-380.
    • (1996) Comp. Chem. , vol.27 , pp. 359-380
    • Brown, N.P.1    Orengo, C.A.2    Taylor, W.R.3
  • 7
    • 34447292490 scopus 로고    scopus 로고
    • Geometric methods for protein structure comparison. Protein structure analysis and design
    • C. Guerra and S. Istrail, eds., Springer-Verlag, New York
    • Ferrari, C., and Guerra, C. 2003. Geometric methods for protein structure comparison. Protein structure analysis and design, in C. Guerra and S. Istrail, eds., Lecture Notes in Bioinformatics, Springer-Verlag, New York.
    • (2003) Lecture Notes in Bioinformatics
    • Ferrari, C.1    Guerra, C.2
  • 8
    • 0142105882 scopus 로고    scopus 로고
    • A Grid-aware approach to protein structure comparison
    • Special Issue on "High Performance Computational Biology."
    • Ferrari, C., Guerra, C., and Zanotti, G. 2003. A Grid-aware approach to protein structure comparison. J. Parallel and Distributed Computing, Special Issue on "High Performance Computational Biology."
    • (2003) J. Parallel and Distributed Computing
    • Ferrari, C.1    Guerra, C.2    Zanotti, G.3
  • 9
    • 0029564871 scopus 로고
    • A 3D sequence-independent representation of the protein data bank
    • Fischer, D., Tsai, C.J., Nussinov, R., and Wolfson, H. 1995. A 3D sequence-independent representation of the protein data bank. Protein Eng. 8, 981-997.
    • (1995) Protein Eng. , vol.8 , pp. 981-997
    • Fischer, D.1    Tsai, C.J.2    Nussinov, R.3    Wolfson, H.4
  • 11
    • 0001073978 scopus 로고
    • A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites
    • Gerstein, M. 1992. A resolution-sensitive procedure for comparing protein surfaces and its application to the comparison of antigen-combining sites. Acta Cryst. A8, 271-276.
    • (1992) Acta Cryst. , vol.A8 , pp. 271-276
    • Gerstein, M.1
  • 12
    • 0031938039 scopus 로고    scopus 로고
    • Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins
    • Gerstein, M., and Levitt, M. 1998. Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins. Protein Sci. 7, 445-456.
    • (1998) Protein Sci. , vol.7 , pp. 445-456
    • Gerstein, M.1    Levitt, M.2
  • 13
    • 0029936121 scopus 로고    scopus 로고
    • Surprising similarities in structure comparison
    • Gibrat, J.F., Madej, T., and Bryant, S.H. 1996. Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 6(3), 377-385.
    • (1996) Curr. Opin. Struct. Biol. , vol.6 , Issue.3 , pp. 377-385
    • Gibrat, J.F.1    Madej, T.2    Bryant, S.H.3
  • 14
    • 0027511808 scopus 로고
    • Identification of tertiary structure resemblance in proteins using a maxima common subgraph isomorphism algorithm
    • Grindley, H.M., Artymiuk, P.J., Rice, D.W., and Willen, P. 1993. Identification of tertiary structure resemblance in proteins using a maxima common subgraph isomorphism algorithm. J. Mol. Biol. 229, 707-721.
    • (1993) J. Mol. Biol. , vol.229 , pp. 707-721
    • Grindley, H.M.1    Artymiuk, P.J.2    Rice, D.W.3    Willen, P.4
  • 17
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm, L., and Sander, C. 1996. Mapping the protein universe. Science 273, 595-602.
    • (1996) Science , vol.273 , pp. 595-602
    • Holm, L.1    Sander, C.2
  • 18
    • 0029918694 scopus 로고    scopus 로고
    • The FSSP database: Fold classification based on structure-structure alignment of proteins
    • Holm, L., and Sander, C. 1996b. The FSSP database: Fold classification based on structure-structure alignment of proteins. Nucl. Acids Res. 24(1), 206-209.
    • (1996) Nucl. Acids Res. , vol.24 , Issue.1 , pp. 206-209
    • Holm, L.1    Sander, C.2
  • 19
    • 84975553202 scopus 로고
    • Closed-form solution of absolute orientation using unit quaternions
    • Horn, B.K.P. 1987. Closed-form solution of absolute orientation using unit quaternions. J. Opt. Soc. Am. 4(4), 629-642.
    • (1987) J. Opt. Soc. Am. , vol.4 , Issue.4 , pp. 629-642
    • Horn, B.K.P.1
  • 21
    • 0034826884 scopus 로고    scopus 로고
    • Optimal PDB structure alignments: A branch-and-cut algorithm for the maximum contact map overlap problem
    • Lancia, G., Carr, R., Walenz, B., and Istrail, S. 2001. Optimal PDB structure alignments: A branch-and-cut algorithm for the maximum contact map overlap problem. Proc. 5th ACM Research in Computational Biology, 193-202.
    • (2001) Proc. 5th ACM Research in Computational Biology , pp. 193-202
    • Lancia, G.1    Carr, R.2    Walenz, B.3    Istrail, S.4
  • 22
    • 0034065350 scopus 로고    scopus 로고
    • Computational methods for the structural alignment of molecules
    • Lemmen, C., Lengauer, T. 2000. Computational methods for the structural alignment of molecules. J. Computer-Aided Molecular Design 14, 215-232.
    • (2000) J. Computer-Aided Molecular Design , vol.14 , pp. 215-232
    • Lemmen, C.1    Lengauer, T.2
  • 23
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E., Hubbard, T., and Chothia, C. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 24
    • 0347719528 scopus 로고    scopus 로고
    • Evaluation of protein fold comparison servers
    • Novotny, M., Madsen, D., and Kleywegt, G.J. 2004. Evaluation of protein fold comparison servers. Proteins 54, 260-270.
    • (2004) Proteins , vol.54 , pp. 260-270
    • Novotny, M.1    Madsen, D.2    Kleywegt, G.J.3
  • 25
    • 0027293521 scopus 로고
    • Molecular recognition in protein families: A database of aligned three-dimensional structures of related proteins
    • Overington, J.P., Zhu, Z.Y., Sali, A., Johnson, M.S., Sowdhamini, R., Louie, G.V., and Blundell, T.L. 1993. Molecular recognition in protein families: A database of aligned three-dimensional structures of related proteins. Biochem. Soc. Trans. 21(3), 597-604.
    • (1993) Biochem. Soc. Trans. , vol.21 , Issue.3 , pp. 597-604
    • Overington, J.P.1    Zhu, Z.Y.2    Sali, A.3    Johnson, M.S.4    Sowdhamini, R.5    Louie, G.V.6    Blundell, T.L.7
  • 27
    • 0025317502 scopus 로고
    • Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relations through simulated annealing and dynamic programming
    • Sali, A., Blundell, P.T.L. 1990. Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relations through simulated annealing and dynamic programming. J. Mol. Biol. 212(2), 403-428.
    • (1990) J. Mol. Biol. , vol.212 , Issue.2 , pp. 403-428
    • Sali, A.1    Blundell, P.T.L.2
  • 28
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov, I.N., and Bourne, P.E. 1998. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11(9), 739-747.
    • (1998) Protein Eng. , vol.11 , Issue.9 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 29
    • 0030628304 scopus 로고    scopus 로고
    • Hierarchical protein structure superposition using both secondary structures and atomic representations
    • Singh, A.P., and Brutlag, D.L. 1997. Hierarchical protein structure superposition using both secondary structures and atomic representations. Proc. 5th Int. Conf. Intell. Sys. Mol. Biol. 284-293.
    • (1997) Proc. 5th Int. Conf. Intell. Sys. Mol. Biol. , pp. 284-293
    • Singh, A.P.1    Brutlag, D.L.2
  • 30
    • 0033011876 scopus 로고    scopus 로고
    • Protein structure comparison using iterated double dynamic programming
    • Taylor, W.R. 1999. Protein structure comparison using iterated double dynamic programming. Protein Sci. 8, 654-665.
    • (1999) Protein Sci. , vol.8 , pp. 654-665
    • Taylor, W.R.1
  • 31
    • 0024349252 scopus 로고
    • Protein structure alignment
    • Taylor, W.R., and Orengo, C.A. 1989. Protein structure alignment. J. Mol. Biol. 208(1), 1-22.
    • (1989) J. Mol. Biol. , vol.208 , Issue.1 , pp. 1-22
    • Taylor, W.R.1    Orengo, C.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.