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Volumn 37, Issue 1, 1999, Pages 20-29

Toward more meaningful hierarchical classification of protein three- dimensional structures

Author keywords

Clustering; Protein fold; Protein structure similarity measure; Tree diagram; Validation

Indexed keywords

GLOBIN; SERINE PROTEINASE INHIBITOR;

EID: 0033214429     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991001)37:1<20::AID-PROT3>3.0.CO;2-V     Document Type: Article
Times cited : (25)

References (71)
  • 1
    • 16044367245 scopus 로고    scopus 로고
    • Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii
    • Bult CJ, White O, Olsen GJ, et al. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 1996;273:1058-1073.
    • (1996) Science , vol.273 , pp. 1058-1073
    • Bult, C.J.1    White, O.2    Olsen, G.J.3
  • 4
    • 0345508435 scopus 로고    scopus 로고
    • Family feuds
    • Lewin R. Family feuds. New Sci 1998;2118:36-40.
    • (1998) New Sci , vol.2118 , pp. 36-40
    • Lewin, R.1
  • 5
    • 0004206243 scopus 로고    scopus 로고
    • Cambridge (MA): Blackwell Science
    • Ridley M. Evolution (2nd ed.). Cambridge (MA): Blackwell Science; 1996.
    • (1996) Evolution (2nd Ed.)
    • Ridley, M.1
  • 6
    • 0030910802 scopus 로고    scopus 로고
    • Structural trees for protein superfamilies
    • Efimov AV. Structural trees for protein superfamilies. Proteins 1997;28:241-260.
    • (1997) Proteins , vol.28 , pp. 241-260
    • Efimov, A.V.1
  • 7
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm L, Sander C. Mapping the protein universe. Science 1996;273: 595-602.
    • (1996) Science , vol.273 , pp. 595-602
    • Holm, L.1    Sander, C.2
  • 8
    • 0028961335 scopus 로고
    • SCOP - A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C. SCOP - a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995;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
  • 9
    • 0027533260 scopus 로고
    • Globin fold in a bacterial toxin
    • Holm L, Sander C. Globin fold in a bacterial toxin. Nature 1993;361:309.
    • (1993) Nature , vol.361 , pp. 309
    • Holm, L.1    Sander, C.2
  • 10
    • 0027451713 scopus 로고
    • A local alignment method for protein structure motifs
    • Orengo CA, Taylor WR. A local alignment method for protein structure motifs. J Mol Biol 1993;233:488-497.
    • (1993) J Mol Biol , vol.233 , pp. 488-497
    • Orengo, C.A.1    Taylor, W.R.2
  • 13
    • 0002478960 scopus 로고    scopus 로고
    • Hierarchical classification
    • Arabie P, Hubert LJ, De Soete G, editors. Singapore: World Scientific
    • Gordon AD. Hierarchical classification. In: Arabie P, Hubert LJ, De Soete G, editors. Clustering and classification. Singapore: World Scientific; 1996. p 65-121.
    • (1996) Clustering and Classification , pp. 65-121
    • Gordon, A.D.1
  • 14
    • 0344458819 scopus 로고    scopus 로고
    • Introduction
    • Arabie P, Hubert LJ, De Soete G, editors. Singapore: World Scientific
    • Hartigan JA. Introduction. In: Clustering and classification. Arabie P, Hubert LJ, De Soete G, editors. Singapore: World Scientific; 1996. p 1-3.
    • (1996) Clustering and Classification , pp. 1-3
    • Hartigan, J.A.1
  • 16
    • 0021160693 scopus 로고
    • The alignment of sets of sequences and the construction of phyletic trees - An integrated method
    • Hogeweg P, Hesper B. The alignment of sets of sequences and the construction of phyletic trees - an integrated method. J Mol Evol 1984;20:175-186.
    • (1984) J Mol Evol , vol.20 , pp. 175-186
    • Hogeweg, P.1    Hesper, B.2
  • 17
    • 0023518540 scopus 로고
    • A strategy for the rapid multiple alignment of protein sequences - Confidence levels from tertiary structure
    • Barton GJ, Sternberg MJE. A strategy for the rapid multiple alignment of protein sequences - confidence levels from tertiary structure. J Mol Biol 1987;198:327-337.
    • (1987) J Mol Biol , vol.198 , pp. 327-337
    • Barton, G.J.1    Sternberg, M.J.E.2
  • 18
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng DF, Doolittle RF. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 1987;25:351-360.
    • (1987) J Mol Evol , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 19
    • 0024245156 scopus 로고
    • A flexible method to align large numbers of biological sequences
    • Taylor WR. A flexible method to align large numbers of biological sequences. J Mol Evol 1988;28:161-169.
    • (1988) J Mol Evol , vol.28 , pp. 161-169
    • Taylor, W.R.1
  • 20
    • 0027968068 scopus 로고
    • CLUSTAL-W - Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ. CLUSTAL-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994;22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 21
    • 0025317502 scopus 로고
    • Definition of general topological equivalence in protein structures - A procedure involving comparison of properties and relationships through simulated annealing and dynamic-programming
    • Šali A, Blundell TL. Definition of general topological equivalence in protein structures - a procedure involving comparison of properties and relationships through simulated annealing and dynamic-programming. J Mol Biol 1990;212:403-428.
    • (1990) J Mol Biol , vol.212 , pp. 403-428
    • Šali, A.1    Blundell, T.L.2
  • 22
    • 0026743174 scopus 로고
    • Multiple protein sequence alignment from tertiary structure comparison - Assignment of global and residue confidence levels
    • Russell RB, Barton GJ. Multiple protein sequence alignment from tertiary structure comparison - assignment of global and residue confidence levels. Proteins 1992;14:309-323.
    • (1992) Proteins , vol.14 , pp. 309-323
    • Russell, R.B.1    Barton, G.J.2
  • 24
    • 0029564172 scopus 로고
    • Improved genetic algorithm-based protein structure comparisons: Pairwise and multiple superpositions
    • May ACW, Johnson MS. Improved genetic algorithm-based protein structure comparisons: pairwise and multiple superpositions. Protein Eng 1995;8:873-882.
    • (1995) Protein Eng , vol.8 , pp. 873-882
    • May, A.C.W.1    Johnson, M.S.2
  • 25
    • 0028914725 scopus 로고
    • An automatic method involving cluster-analysis of secondary structures for the identification of domains in proteins
    • Sowdhamini R, Blundell TL. An automatic method involving cluster-analysis of secondary structures for the identification of domains in proteins. Protein Sci 1995;4:506-520.
    • (1995) Protein Sci , vol.4 , pp. 506-520
    • Sowdhamini, R.1    Blundell, T.L.2
  • 26
    • 0030596489 scopus 로고    scopus 로고
    • A global taxonomy of loops in globular proteins
    • Kwasigroch JM, Chomilier J, Mornon JP. A global taxonomy of loops in globular proteins. J Mol Biol 1996;259:855-872.
    • (1996) J Mol Biol , vol.259 , pp. 855-872
    • Kwasigroch, J.M.1    Chomilier, J.2    Mornon, J.P.3
  • 27
    • 0030589039 scopus 로고    scopus 로고
    • Structural families in loops of homologous proteins - Automatic classification, modeling and application to antibodies
    • Martin ACR, Thornton JM. Structural families in loops of homologous proteins - automatic classification, modeling and application to antibodies. J Mol Biol 1996;263:800-815.
    • (1996) J Mol Biol , vol.263 , pp. 800-815
    • Martin, A.C.R.1    Thornton, J.M.2
  • 28
    • 0030449155 scopus 로고    scopus 로고
    • Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction
    • Donate LE, Rufino SD, Canard LHJ, Blundell TL. Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction. Protein Sci 1996;5:2600-2616.
    • (1996) Protein Sci , vol.5 , pp. 2600-2616
    • Donate, L.E.1    Rufino, S.D.2    Canard, L.H.J.3    Blundell, T.L.4
  • 30
    • 0028991962 scopus 로고
    • Modeling mutations and homologous proteins
    • Šali, A. Modeling mutations and homologous proteins. Curr Opin Biotech 1995;6:437-451.
    • (1995) Curr Opin Biotech , vol.6 , pp. 437-451
  • 31
    • 0027361123 scopus 로고
    • A structural basis for sequence comparisons - An evaluation of scoring methodologies
    • Johnson MS, Overington JP. A structural basis for sequence comparisons - an evaluation of scoring methodologies. J Mol Biol 1993;233:716-738.
    • (1993) J Mol Biol , vol.233 , pp. 716-738
    • Johnson, M.S.1    Overington, J.P.2
  • 32
    • 0031566432 scopus 로고    scopus 로고
    • Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation
    • Russell RB, Saqi MAS, Sayle RA, Bates PA, Sternberg MJE. Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J Mol Biol 1997;269:423-439.
    • (1997) J Mol Biol , vol.269 , pp. 423-439
    • Russell, R.B.1    Saqi, M.A.S.2    Sayle, R.A.3    Bates, P.A.4    Sternberg, M.J.E.5
  • 33
    • 0025744920 scopus 로고
    • Detection of common 3-dimensional substructures in proteins
    • Vriend G, Sander C. Detection of common 3-dimensional substructures in proteins. Proteins 1991;11:52-58.
    • (1991) Proteins , vol.11 , pp. 52-58
    • Vriend, G.1    Sander, C.2
  • 34
    • 0028789439 scopus 로고
    • Optimal protein structure alignments by multiple linkage clustering - Application to distantly related proteins
    • Boutonnet NS, Rooman MJ, Ochagavia ME, Richelle J, Wodak SJ. Optimal protein structure alignments by multiple linkage clustering - application to distantly related proteins. Protein Eng 1995;8: 647-662.
    • (1995) Protein Eng , vol.8 , pp. 647-662
    • Boutonnet, N.S.1    Rooman, M.J.2    Ochagavia, M.E.3    Richelle, J.4    Wodak, S.J.5
  • 35
    • 0028319318 scopus 로고
    • Classification of protein folds
    • Orengo CA. Classification of protein folds. Curr Opin Struct Biol 1994;4:429-440.
    • (1994) Curr Opin Struct Biol , vol.4 , pp. 429-440
    • Orengo, C.A.1
  • 36
    • 0030448595 scopus 로고    scopus 로고
    • Pairwise iterative superposition of distantly related proteins and assessment of the significance of 3-D structural similarity
    • May ACW. Pairwise iterative superposition of distantly related proteins and assessment of the significance of 3-D structural similarity. Protein Eng 1996;9:1093-1101.
    • (1996) Protein Eng , vol.9 , pp. 1093-1101
    • May, A.C.W.1
  • 37
    • 0029091249 scopus 로고    scopus 로고
    • Average core structures and variability measures for protein families - Application to the immunoglobulins
    • Gerstein M, Altman RB. Average core structures and variability measures for protein families - application to the immunoglobulins. J Mol Biol 251:161-175.
    • J Mol Biol , vol.251 , pp. 161-175
    • Gerstein, M.1    Altman, R.B.2
  • 38
    • 0031560777 scopus 로고    scopus 로고
    • Contact area difference (CAD): A robust measure to evaluate accuracy of protein models
    • Abagyan RA, Totrov MM. Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. J Mol Biol 1997;268:678-685.
    • (1997) J Mol Biol , vol.268 , pp. 678-685
    • Abagyan, R.A.1    Totrov, M.M.2
  • 39
    • 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 1993;233:123-138.
    • (1993) J Mol Biol , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 40
    • 0029921425 scopus 로고    scopus 로고
    • A surface of minimum area metric for the structural comparison of proteins
    • Falicov A, Cohen FE. A surface of minimum area metric for the structural comparison of proteins. J Mol Biol 1996;258:871-892.
    • (1996) J Mol Biol , vol.258 , pp. 871-892
    • Falicov, A.1    Cohen, F.E.2
  • 41
    • 0030348027 scopus 로고    scopus 로고
    • A database of globular protein structural domains: Clustering of representative family members into similar folds
    • Sowdhamini R, Rufino SD, Blundell TL. A database of globular protein structural domains: clustering of representative family members into similar folds. Fold Design 1996;1:209-220.
    • (1996) Fold Design , vol.1 , pp. 209-220
    • Sowdhamini, R.1    Rufino, S.D.2    Blundell, T.L.3
  • 42
    • 0000122573 scopus 로고
    • PHYLIP - Phylogeny Inference Package (version 3.2)
    • Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989;5:164-166.
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 43
  • 44
    • 0000461280 scopus 로고
    • Confidence limits on phylogenies - An approach using the bootstrap
    • Felsenstein J. Confidence limits on phylogenies - an approach using the bootstrap. Evolution 1985;39:783-791.
    • (1985) Evolution , vol.39 , pp. 783-791
    • Felsenstein, J.1
  • 45
    • 0027983037 scopus 로고
    • Convergent evolution - The need to be explicit
    • Doolittle RF. Convergent evolution - the need to be explicit. Trends Biochem Sci 1994;19:15-18.
    • (1994) Trends Biochem Sci , vol.19 , pp. 15-18
    • Doolittle, R.F.1
  • 46
    • 0000007888 scopus 로고
    • Detecting internal inconsistencies in distance data
    • Lanyon SM. Detecting internal inconsistencies in distance data. Syst Zool 1985;34:397-403.
    • (1985) Syst Zool , vol.34 , pp. 397-403
    • Lanyon, S.M.1
  • 48
    • 0031022601 scopus 로고    scopus 로고
    • LPFC: An Internet library of protein family core structures
    • Schmidt R, Gerstein M, Altman RB. LPFC: an Internet library of protein family core structures. Protein Sci 1997; 6:246-248.
    • (1997) Protein Sci , vol.6 , pp. 246-248
    • Schmidt, R.1    Gerstein, M.2    Altman, R.B.3
  • 49
    • 0027293521 scopus 로고
    • Molecular recognition in protein families - A database of aligned 3-dimensional structures of related proteins
    • Overington JP, Zhu ZY, Šali A, et al. Molecular recognition in protein families - a database of aligned 3-dimensional structures of related proteins. Biochem Soc Trans 1993;21:597-604.
    • (1993) Biochem Soc Trans , vol.21 , pp. 597-604
    • Overington, J.P.1    Zhu, Z.Y.2    Šali, A.3
  • 50
    • 0028051828 scopus 로고
    • Derivation of rules for comparative protein modeling from a database of protein structure alignments
    • Šali A, Overington JP. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci 1994;3:1582-1596.
    • (1994) Protein Sci , vol.3 , pp. 1582-1596
    • Šali, A.1    Overington, J.P.2
  • 51
    • 0024349252 scopus 로고
    • Protein structure alignment
    • Taylor WR, Orengo CA. Protein structure alignment. J Mol Biol 1989;208:1-22.
    • (1989) J Mol Biol , vol.208 , pp. 1-22
    • Taylor, W.R.1    Orengo, C.A.2
  • 52
    • 0027053207 scopus 로고
    • On the multiple simultaneous superposition of molecular structures by rigid body transformations
    • Diamond R. On the multiple simultaneous superposition of molecular structures by rigid body transformations. Protein Sci 1992;1: 1279-1287.
    • (1992) Protein Sci , vol.1 , pp. 1279-1287
    • Diamond, R.1
  • 53
    • 0028808762 scopus 로고
    • An approach to protein homology modeling based on an ensemble of NMR structures -application to the sox-5 HMG-box protein
    • Adzhubei AA, Laughton CA, Neidle S. An approach to protein homology modeling based on an ensemble of NMR structures -application to the sox-5 HMG-box protein. Protein Eng 1995;8:615-625.
    • (1995) Protein Eng , vol.8 , pp. 615-625
    • Adzhubei, A.A.1    Laughton, C.A.2    Neidle, S.3
  • 54
    • 0029831680 scopus 로고    scopus 로고
    • An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies
    • Kelley LA, Gardner SP, Sutcliffe MJ. An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies. Protein Eng. 9: 1063-1065, 1996.
    • (1996) Protein Eng. , vol.9 , pp. 1063-1065
    • Kelley, L.A.1    Gardner, S.P.2    Sutcliffe, M.J.3
  • 55
    • 0001505364 scopus 로고
    • Superimposing several sets of atomic coordinates
    • Gerber PR, Muller K. Superimposing several sets of atomic coordinates. Acta Crystallogr A 1987;43:426-428.
    • (1987) Acta Crystallogr A , vol.43 , pp. 426-428
    • Gerber, P.R.1    Muller, K.2
  • 56
    • 84986450020 scopus 로고
    • An algorithm for the simultaneous superposition of a structural series
    • Kearsley S.K. An algorithm for the simultaneous superposition of a structural series. J Comp Chem 1990;11:1187-1192.
    • (1990) J Comp Chem , vol.11 , pp. 1187-1192
    • Kearsley, S.K.1
  • 58
    • 0002855179 scopus 로고
    • Coordinate-based cluster analysis
    • Diamond R. Coordinate-based cluster analysis. Acta Crystallogr D 1995;51:127-135.
    • (1995) Acta Crystallogr D , vol.51 , pp. 127-135
    • Diamond, R.1
  • 59
    • 0030843113 scopus 로고    scopus 로고
    • An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures
    • Kelley LA, Gardner SP, Sutcliffe MJ. An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures. Protein Eng 1997;10:737-741.
    • (1997) Protein Eng , vol.10 , pp. 737-741
    • Kelley, L.A.1    Gardner, S.P.2    Sutcliffe, M.J.3
  • 60
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J 1986;5:823-826.
    • (1986) EMBO J , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 61
    • 0030763376 scopus 로고    scopus 로고
    • Estimation of evolutionary distances from protein spatial structures
    • Grishin NV. Estimation of evolutionary distances from protein spatial structures. J Mol Evol 1997;45:359-369.
    • (1997) J Mol Evol , vol.45 , pp. 359-369
    • Grishin, N.V.1
  • 62
    • 0002271592 scopus 로고    scopus 로고
    • Hierarchical classification
    • Arabie P, Hubert LJ, De Soete G, editors. Singapore: World Scientific
    • Milligan GW. Hierarchical classification. In: Arabie P, Hubert LJ, De Soete G, editors. Clustering and classification. Singapore: World Scientific; 1996. p 341-375.
    • (1996) Clustering and Classification , pp. 341-375
    • Milligan, G.W.1
  • 63
    • 85088333883 scopus 로고    scopus 로고
    • Towards more meaningful hierarchical classification of amino acid scoring matrices
    • in press
    • May ACW. Towards more meaningful hierarchical classification of amino acid scoring matrices. Protein Eng (in press).
    • Protein Eng
    • May, A.C.W.1
  • 64
    • 0025104478 scopus 로고
    • Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
    • Overington JP, Johnson MS, Šali A, Blundell TL. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc R Soc Lond B 1990;241: 132-145.
    • (1990) Proc R Soc Lond B , vol.241 , pp. 132-145
    • Overington, J.P.1    Johnson, M.S.2    Šali, A.3    Blundell, T.L.4
  • 65
    • 0026661145 scopus 로고
    • Selection of a representative set of structures from Brookhaven Protein Data-Bank
    • Boberg J, Salakoski T, Vihinen M. Selection of a representative set of structures from Brookhaven Protein Data-Bank. Proteins 1992; 14:265-276.
    • (1992) Proteins , vol.14 , pp. 265-276
    • Boberg, J.1    Salakoski, T.2    Vihinen, M.3
  • 66
    • 0027102226 scopus 로고
    • OBSTRUCT - A program to obtain largest cliques from a protein-sequence set according to structural resolution and sequence similarity
    • Heringa J, Sommerfeldt H, Higgins D, Argos P. OBSTRUCT - a program to obtain largest cliques from a protein-sequence set according to structural resolution and sequence similarity. CABIOS 1992;8:599-600.
    • (1992) CABIOS , vol.8 , pp. 599-600
    • Heringa, J.1    Sommerfeldt, H.2    Higgins, D.3    Argos, P.4
  • 68
    • 0025270037 scopus 로고
    • Phylogenetic relationships from 3-dimensional protein structures
    • Johnson MS, Šali A, Blundell TL. Phylogenetic relationships from 3-dimensional protein structures. Methods Enzymol 1990;183:670-690.
    • (1990) Methods Enzymol , vol.183 , pp. 670-690
    • Johnson, M.S.1    Šali, A.2    Blundell, T.L.3
  • 69
    • 0025070240 scopus 로고
    • Molecular anatomy -phyletic relationships derived from 3-dimensional structures of proteins
    • Johnson MS, Sutcliffe MJ, Blundell TL. Molecular anatomy -phyletic relationships derived from 3-dimensional structures of proteins. J Mol Evol 1990;30:43-59.
    • (1990) J Mol Evol , vol.30 , pp. 43-59
    • Johnson, M.S.1    Sutcliffe, M.J.2    Blundell, T.L.3
  • 70
    • 0017386137 scopus 로고
    • Recognition of phylogenetic relationships from polypeptide chain fold similarities
    • Schulz GE. Recognition of phylogenetic relationships from polypeptide chain fold similarities. J Mol Evol 1977;9:339-342.
    • (1977) J Mol Evol , vol.9 , pp. 339-342
    • Schulz, G.E.1


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