메뉴 건너뛰기




Volumn 12, Issue 12, 2004, Pages 2103-2111

Déjà vu all over again: Finding and analyzing protein structure similarities

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; COMPARATIVE STUDY; DATA BASE; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; REVIEW; SCORING SYSTEM; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 9944251424     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.09.016     Document Type: Note
Times cited : (43)

References (69)
  • 1
    • 0003787146 scopus 로고
    • Princeton, New Jersey: Princeton University Press
    • Bellman R. Dynamic Programming. 1957;Princeton University Press, Princeton, New Jersey
    • (1957) Dynamic Programming
    • Bellman, R.1
  • 3
    • 0035888284 scopus 로고    scopus 로고
    • Universal similarity measure for comparing protein structures
    • Betancourt M.R., Skolnick J. Universal similarity measure for comparing protein structures. Biopolymers. 59:2001;305-309
    • (2001) Biopolymers , vol.59 , pp. 305-309
    • Betancourt, M.R.1    Skolnick, J.2
  • 4
    • 0037267407 scopus 로고    scopus 로고
    • Structure comparison and alignment
    • P.E. Bourne, & H. Weissig. Hoboken, NJ: Wiley-Liss
    • Bourne P.E., Shindyalov I.N. Structure comparison and alignment. Bourne P.E., Weissig H. Structural Bioinformatics. 2004;321-337 Wiley-Liss, Hoboken, NJ
    • (2004) Structural Bioinformatics , pp. 321-337
    • Bourne, P.E.1    Shindyalov, I.N.2
  • 5
    • 0038036593 scopus 로고    scopus 로고
    • How root-mean-square distance (r.m.s.d.) values depend on the resolution of protein structures that are compared
    • Carugo O. How root-mean-square distance (r.m.s.d.) values depend on the resolution of protein structures that are compared. J. Appl. Crystallogr. 36:2003;125-128
    • (2003) J. Appl. Crystallogr. , vol.36 , pp. 125-128
    • Carugo, O.1
  • 6
    • 0034977013 scopus 로고    scopus 로고
    • A normalized root-mean-square distance for comparing protein three-dimensional structures
    • Carugo O., Pongor S. A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein Sci. 10:2001;1470-1473
    • (2001) Protein Sci. , vol.10 , pp. 1470-1473
    • Carugo, O.1    Pongor, S.2
  • 7
    • 0036304230 scopus 로고    scopus 로고
    • Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison
    • Carugo O., Pongor S. Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison. J. Mol. Biol. 315:2002;887-898
    • (2002) J. Mol. Biol. , vol.315 , pp. 887-898
    • Carugo, O.1    Pongor, S.2
  • 8
    • 0001679473 scopus 로고    scopus 로고
    • Align: A program to superimpose protein coordinates, accounting for insertions and deletions
    • Cohen G.H. Align. a program to superimpose protein coordinates, accounting for insertions and deletions J. Appl. Crystallogr. 30:1997;1160-1161
    • (1997) J. Appl. Crystallogr. , vol.30 , pp. 1160-1161
    • Cohen, G.H.1
  • 10
    • 0033106268 scopus 로고    scopus 로고
    • Remarks about protein structure precision
    • Cruickshank D.W.J. Remarks about protein structure precision. Acta Crystallogr. D55:1999;1108
    • (1999) Acta Crystallogr. , vol.55 , pp. 1108
    • Cruickshank, D.W.J.1
  • 12
    • 0002855179 scopus 로고
    • Coordinate-based cluster analysis
    • Diamond R. Coordinate-based cluster analysis. Acta Crystallogr. D51:1995;127-135
    • (1995) Acta Crystallogr. , vol.51 , pp. 127-135
    • Diamond, R.1
  • 13
    • 0142210126 scopus 로고    scopus 로고
    • Multiple structural alignment by secondary structures: Algorithm and applications
    • Dror O., Benyamini H., Nussinov R., Wolfson H.J. Multiple structural alignment by secondary structures. algorithm and applications Protein Sci. 12:2003;2492-2507
    • (2003) Protein Sci. , vol.12 , pp. 2492-2507
    • Dror, O.1    Benyamini, H.2    Nussinov, R.3    Wolfson, H.J.4
  • 15
    • 0030310317 scopus 로고    scopus 로고
    • Assessing the performance of fold recognition methods by means of a comprehensive benchmark
    • Fischer, D., Elofsson, A., Rice, D., and Eisenberg, D. (1996). Assessing the performance of fold recognition methods by means of a comprehensive benchmark. Pacific Symposium on Biocomputing, 300-318.
    • (1996) Pacific Symposium on Biocomputing , pp. 300-318
    • Fischer, D.1    Elofsson, A.2    Rice, D.3    Eisenberg, D.4
  • 16
    • 0031938039 scopus 로고    scopus 로고
    • Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins
    • Gerstein M., Levitt M. Comprehensive assessment of automatic structural alignment against a manual standard, the scop classification of proteins. Protein Sci. 7:1998;445-456
    • (1998) Protein Sci. , vol.7 , pp. 445-456
    • Gerstein, M.1    Levitt, M.2
  • 18
    • 0032906118 scopus 로고    scopus 로고
    • Motif-based searching in TOPS protein topology databases
    • Gilbert D., Westhead D., Nagano N., Thornton J. Motif-based searching in TOPS protein topology databases. Bioinformatics. 15:1999;317-326
    • (1999) Bioinformatics , vol.15 , pp. 317-326
    • Gilbert, D.1    Westhead, D.2    Nagano, N.3    Thornton, J.4
  • 19
    • 0033200307 scopus 로고    scopus 로고
    • A systematic comparison of protein structure classifications: SCOP, CATH and FSSP
    • Hadley C., Jones D.T. A systematic comparison of protein structure classifications. SCOP, CATH and FSSP Struct. Fold. Des. 7:1999;1099-1112
    • (1999) Struct. Fold. Des. , vol.7 , pp. 1099-1112
    • Hadley, C.1    Jones, D.T.2
  • 21
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 22
    • 0028290005 scopus 로고
    • Parser for protein folding units
    • Holm L., Sander C. Parser for protein folding units. Proteins. 19:1994;256-268
    • (1994) Proteins , vol.19 , pp. 256-268
    • Holm, L.1    Sander, C.2
  • 23
    • 0031865006 scopus 로고    scopus 로고
    • Touring protein fold space with Dali/FSSP
    • Holm L., Sander C. Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 26:1998;316-319
    • (1998) Nucleic Acids Res. , vol.26 , pp. 316-319
    • Holm, L.1    Sander, C.2
  • 24
    • 0015023470 scopus 로고
    • The atomic structure of erythrocruorin in the light of the chemical sequence and its comparison with myoglobin
    • Huber R., Epp O., Steigemann W., Formanek H. The atomic structure of erythrocruorin in the light of the chemical sequence and its comparison with myoglobin. Eur. J. Biochem. 19:1971;42-50
    • (1971) Eur. J. Biochem. , vol.19 , pp. 42-50
    • Huber, R.1    Epp, O.2    Steigemann, W.3    Formanek, H.4
  • 25
    • 0031889752 scopus 로고    scopus 로고
    • Domain assignment for protein structures using a consensus approach: Characterization and analysis
    • Jones S., Stewart M., Michie A., Swindells M.B., Orengo C., Thornton J.M. Domain assignment for protein structures using a consensus approach. characterization and analysis Protein Sci. 7:1998;233-242
    • (1998) Protein Sci. , vol.7 , pp. 233-242
    • Jones, S.1    Stewart, M.2    Michie, A.3    Swindells, M.B.4    Orengo, C.5    Thornton, J.M.6
  • 26
    • 0033833116 scopus 로고    scopus 로고
    • Protein structure alignment using environmental profiles
    • Jung J., Lee B. Protein structure alignment using environmental profiles. Protein Eng. 13:2000;535-543
    • (2000) Protein Eng. , vol.13 , pp. 535-543
    • Jung, J.1    Lee, B.2
  • 27
    • 84893482610 scopus 로고
    • A solution for the best rotation to relate two sets of vectors
    • Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A32:1976;922-923
    • (1976) Acta Crystallogr. , vol.32 , pp. 922-923
    • Kabsch, W.1
  • 28
    • 12944249776 scopus 로고
    • A discussion of the solution for the best rotation to relate two sets of vectors
    • Kabsch W. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A34:1978;827-828
    • (1978) Acta Crystallogr. , vol.34 , pp. 827-828
    • Kabsch, W.1
  • 29
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin S., Altschul S.F. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA. 87:1990;2264-2268
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 30
    • 0034308164 scopus 로고    scopus 로고
    • Protein structure comparison using the markov transition model of evolution
    • Kawabata T., Nishikawa K. Protein structure comparison using the markov transition model of evolution. Proteins. 41:2000;108-122
    • (2000) Proteins , vol.41 , pp. 108-122
    • Kawabata, T.1    Nishikawa, K.2
  • 31
    • 0030501419 scopus 로고    scopus 로고
    • Use of non-crystallographic symmetry in protein structure refinement
    • Kleywegt G.J. Use of non-crystallographic symmetry in protein structure refinement. Acta Crystallogr. D52:1996;842-857
    • (1996) Acta Crystallogr. , vol.52 , pp. 842-857
    • Kleywegt, G.J.1
  • 32
    • 0030841589 scopus 로고    scopus 로고
    • Detecting folding motifs and similarities in protein structures
    • Kleywegt G.J., Jones T.A. Detecting folding motifs and similarities in protein structures. Methods Enzymol. 277:1997;525-545
    • (1997) Methods Enzymol. , vol.277 , pp. 525-545
    • Kleywegt, G.J.1    Jones, T.A.2
  • 33
    • 1842781469 scopus 로고    scopus 로고
    • Protein structure comparison in 3D based on secondary structure matching (SSM) followed by Ca alignment, scored by a new structural similarity function
    • Paper presented (Vienna, Austria).
    • Krissinel, E., and Henrick, K. (2003). Protein structure comparison in 3D based on secondary structure matching (SSM) followed by Ca alignment, scored by a new structural similarity function. Paper presented at: Proceedings of the 5th International Conference on Molecular Structural Biology (Vienna, Austria).
    • (2003) Proceedings of the 5th International Conference on Molecular Structural Biology
    • Krissinel, E.1    Henrick, K.2
  • 35
    • 0035874115 scopus 로고    scopus 로고
    • Automated multiple structure alignment and detection of a common substructural motif
    • Leibowitz N., Fligelman Z.Y., Nussinov R., Wolfson H.J. Automated multiple structure alignment and detection of a common substructural motif. Proteins. 43:2001;235-245
    • (2001) Proteins , vol.43 , pp. 235-245
    • Leibowitz, N.1    Fligelman, Z.Y.2    Nussinov, R.3    Wolfson, H.J.4
  • 36
    • 0032568649 scopus 로고    scopus 로고
    • A unified statistical framework for sequence comparison and structure comparison
    • Levitt M., Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proc. Natl. Acad. Sci. USA. 95:1998;5913-5920
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 5913-5920
    • Levitt, M.1    Gerstein, M.2
  • 37
    • 0034479757 scopus 로고    scopus 로고
    • Top: A new method for protein structure comparisons and similarity searches
    • Lu G. Top. a new method for protein structure comparisons and similarity searches J. Appl. Crystallogr. 33:2000;176-183
    • (2000) J. Appl. Crystallogr. , vol.33 , pp. 176-183
    • Lu, G.1
  • 38
    • 0028838717 scopus 로고
    • Threading a database of protein cores
    • Madej T., Gibrat J.F., Bryant S.H. Threading a database of protein cores. Proteins. 23:1995;356-369
    • (1995) Proteins , vol.23 , pp. 356-369
    • Madej, T.1    Gibrat, J.F.2    Bryant, S.H.3
  • 39
    • 0034458972 scopus 로고    scopus 로고
    • The ups and downs of protein topology; Rapid comparison of protein structure
    • Martin A.C. The ups and downs of protein topology; rapid comparison of protein structure. Protein Eng. 13:2000;829-837
    • (2000) Protein Eng. , vol.13 , pp. 829-837
    • Martin, A.C.1
  • 40
    • 0033120222 scopus 로고    scopus 로고
    • Identification of homologous core structures
    • Matsuo Y., Bryant S.H. Identification of homologous core structures. Proteins. 35:1999;70-79
    • (1999) Proteins , vol.35 , pp. 70-79
    • Matsuo, Y.1    Bryant, S.H.2
  • 42
    • 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., Chothia C. Scop. a structural classification of proteins database for the investigation of sequences and structures J. Mol. Biol. 247:1995;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
  • 43
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman S.B., Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48:1970;443-453
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 44
    • 0347719528 scopus 로고    scopus 로고
    • Evaluation of protein fold comparison servers
    • Novotny M., Madsen D., Kleywegt G.J. Evaluation of protein fold comparison servers. Proteins. 54:2004;260-270
    • (2004) Proteins , vol.54 , pp. 260-270
    • Novotny, M.1    Madsen, D.2    Kleywegt, G.J.3
  • 45
    • 0025719208 scopus 로고
    • Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques
    • Nussinov R., Wolfson H.J. Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc. Natl. Acad. Sci. USA. 88:1991;10495-10499
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 10495-10499
    • Nussinov, R.1    Wolfson, H.J.2
  • 46
    • 0027451713 scopus 로고
    • A local alignment method for protein structure motifs
    • Orengo C., Taylor W.R. A local alignment method for protein structure motifs. J. Mol. Biol. 233:1993;488-497
    • (1993) J. Mol. Biol. , vol.233 , pp. 488-497
    • Orengo, C.1    Taylor, W.R.2
  • 47
    • 0026759751 scopus 로고
    • Fast structure alignment for protein databank searching
    • Orengo C.A., Brown N.P., Taylor W.R. Fast structure alignment for protein databank searching. Proteins. 14:1992;139-167
    • (1992) Proteins , vol.14 , pp. 139-167
    • Orengo, C.A.1    Brown, N.P.2    Taylor, W.R.3
  • 49
    • 0036839162 scopus 로고    scopus 로고
    • MAMMOTH (matching molecular models obtained from theory) an automated method for model comparison
    • Ortiz A.R., Strauss C.E., Olmea O. MAMMOTH (matching molecular models obtained from theory). an automated method for model comparison Protein Sci. 11:2002;2606-2621
    • (2002) Protein Sci. , vol.11 , pp. 2606-2621
    • Ortiz, A.R.1    Strauss, C.E.2    Olmea, O.3
  • 50
    • 0027124186 scopus 로고
    • Signal transduction. Fishing in Src-infested waters
    • Petsko G.A. Signal transduction. Fishing in Src-infested waters. Nature. 358:1992;625-626
    • (1992) Nature , vol.358 , pp. 625-626
    • Petsko, G.A.1
  • 51
    • 0037422619 scopus 로고    scopus 로고
    • Automatic classification of protein structure by using Gauss integrals
    • Rogen P., Fain B. Automatic classification of protein structure by using Gauss integrals. Proc. Natl. Acad. Sci. USA. 100:2003;119-124
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 119-124
    • Rogen, P.1    Fain, B.2
  • 52
    • 0026743174 scopus 로고
    • Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
    • Russell R.B., Barton G.J. Multiple protein sequence alignment from tertiary structure comparison. assignment of global and residue confidence levels Proteins. 14:1992;309-323
    • (1992) Proteins , vol.14 , pp. 309-323
    • Russell, R.B.1    Barton, G.J.2
  • 53
    • 0034084540 scopus 로고    scopus 로고
    • Objective comparison of protein structures: Error-scaled difference distance matrices
    • Schneider T.R. Objective comparison of protein structures. error-scaled difference distance matrices Acta Crystallogr. D56:2000;714-721
    • (2000) Acta Crystallogr. , vol.56 , pp. 714-721
    • Schneider, T.R.1
  • 54
    • 0036008503 scopus 로고    scopus 로고
    • A genetic algorithm for the identification of conformationally invariant regions in protein molecules
    • Schneider T.R. A genetic algorithm for the identification of conformationally invariant regions in protein molecules. Acta Crystallogr. D. 58:2002;195-208
    • (2002) Acta Crystallogr. D , vol.58 , pp. 195-208
    • Schneider, T.R.1
  • 56
    • 0347994105 scopus 로고    scopus 로고
    • FoldMiner: Structural motif discovery using an improved superposition algorithm
    • Shapiro J., Brutlag D. FoldMiner. structural motif discovery using an improved superposition algorithm Protein Sci. 13:2004;278-294
    • (2004) Protein Sci. , vol.13 , pp. 278-294
    • Shapiro, J.1    Brutlag, D.2
  • 57
    • 0036681439 scopus 로고    scopus 로고
    • Flexible protein alignment and hinge detection
    • Shatsky M., Nussinov R., Wolfson H.J. Flexible protein alignment and hinge detection. Proteins. 48:2002;242-256
    • (2002) Proteins , vol.48 , pp. 242-256
    • Shatsky, M.1    Nussinov, R.2    Wolfson, H.J.3
  • 58
    • 0031715982 scopus 로고    scopus 로고
    • Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
    • Shindyalov I.N., Bourne P.E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11:1998;739-747
    • (1998) Protein Eng. , vol.11 , pp. 739-747
    • Shindyalov, I.N.1    Bourne, P.E.2
  • 59
    • 1342289274 scopus 로고    scopus 로고
    • Sensitivity and selectivity in protein structure comparison
    • Sierk M.L., Pearson W.R. Sensitivity and selectivity in protein structure comparison. Protein Sci. 13:2004;773-785
    • (2004) Protein Sci. , vol.13 , pp. 773-785
    • Sierk, M.L.1    Pearson, W.R.2
  • 60
    • 0030628304 scopus 로고    scopus 로고
    • Hierarchical protein structure superposition using both secondary structure and atomic representations
    • Singh A.P., Brutlag D.L. Hierarchical protein structure superposition using both secondary structure and atomic representations. Proc Intelligent Systems for Molecular Biology. 5:1997;284-293
    • (1997) Proc Intelligent Systems for Molecular Biology , vol.5 , pp. 284-293
    • Singh, A.P.1    Brutlag, D.L.2
  • 61
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147:1981;195-197
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 62
    • 0028914725 scopus 로고
    • An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins
    • Sowdhamini R., Blundell T.L. An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci. 4:1995;506-520
    • (1995) Protein Sci. , vol.4 , pp. 506-520
    • Sowdhamini, R.1    Blundell, T.L.2
  • 63
    • 0033997724 scopus 로고    scopus 로고
    • Protein structure alignment using a genetic algorithm
    • Szustakowski J.D., Weng Z. Protein structure alignment using a genetic algorithm. Proteins. 38:2000;428-440
    • (2000) Proteins , vol.38 , pp. 428-440
    • Szustakowski, J.D.1    Weng, Z.2
  • 64
    • 0033011876 scopus 로고    scopus 로고
    • Protein structure comparison using iterated double dynamic programming
    • Taylor W. Protein structure comparison using iterated double dynamic programming. Protein Sci. 8:1999;654-665
    • (1999) Protein Sci. , vol.8 , pp. 654-665
    • Taylor, W.1
  • 65
  • 66
    • 0034677669 scopus 로고    scopus 로고
    • Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
    • Wilson C.A., Kreychman J., Gerstein M. Assessing annotation transfer for genomics. quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores J. Mol. Biol. 297:2000;233-249
    • (2000) J. Mol. Biol. , vol.297 , pp. 233-249
    • Wilson, C.A.1    Kreychman, J.2    Gerstein, M.3
  • 67
    • 0034682881 scopus 로고    scopus 로고
    • An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance
    • Yang A.S., Honig B. An integrated approach to the analysis and modeling of protein sequences and structures. I. Protein structural alignment and a quantitative measure for protein structural distance. J. Mol. Biol. 301:2000;665-678
    • (2000) J. Mol. Biol. , vol.301 , pp. 665-678
    • Yang, A.S.1    Honig, B.2
  • 68
    • 3042581007 scopus 로고    scopus 로고
    • Flexible structure alignment by chaining aligned fragment pairs allowing twists
    • Ye Y., Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. 19(Suppl 2):2003;II246-II255
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Ye, Y.1    Godzik, A.2
  • 69
    • 0031307124 scopus 로고    scopus 로고
    • Numerical criteria for the evaluation of ab initio predictions of protein structure
    • Zemla A., Venclovas C., Reinhardt A., Fidelis K., Hubbard T.J. Numerical criteria for the evaluation of ab initio predictions of protein structure. Proteins. 1:1997;140-150
    • (1997) Proteins , vol.1 , pp. 140-150
    • Zemla, A.1    Venclovas, C.2    Reinhardt, A.3    Fidelis, K.4    Hubbard, T.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.