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Volumn 37, Issue 3, 1999, Pages 360-378

ProtoMap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space

Author keywords

Clustering; Homologous proteins; Protein classification; Protein families; Sequence alignment

Indexed keywords

AMINO ACID; PROTEIN;

EID: 0032726692     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991115)37:3<360::AID-PROT5>3.0.CO;2-Z     Document Type: Article
Times cited : (91)

References (54)
  • 1
    • 0030867578 scopus 로고    scopus 로고
    • Microbial genomes come tumbling in
    • Pennisi E. Microbial genomes come tumbling in. Science 1997;277: 1433.
    • (1997) Science , vol.277 , pp. 1433
    • Pennisi, E.1
  • 2
    • 0032568439 scopus 로고    scopus 로고
    • Microbial genomes opened up
    • Doolittle RF. Microbial genomes opened up. Nature 1998;392:339-342.
    • (1998) Nature , vol.392 , pp. 339-342
    • Doolittle, R.F.1
  • 3
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman SB, Wunsch CD. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 1970;48:443-453.
    • (1970) J Mol Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 5
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity
    • Lipman DJ, Pearson WR. Rapid and sensitive protein similarity. Science 1985;227:1435-1441.
    • (1985) Science , vol.227 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 8
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 1991;9:56-68.
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 9
    • 0027485083 scopus 로고
    • Comparison of conformational characteristics in structurally similar protein pairs
    • Flores TP, Orengo CA, Moss D, Thoronton JM. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci 1993;2:1811-1826.
    • (1993) Protein Sci , vol.2 , pp. 1811-1826
    • Flores, T.P.1    Orengo, C.A.2    Moss, D.3    Thoronton, J.M.4
  • 10
    • 0027363912 scopus 로고
    • Structural relationships of homologous proteins as a fundamental principle in homology modeling
    • Hilbert M, Bohm G, Jaenicke R. Structural relationships of homologous proteins as a fundamental principle in homology modeling. Proteins 1993;17:138-151.
    • (1993) Proteins , vol.17 , pp. 138-151
    • Hilbert, M.1    Bohm, G.2    Jaenicke, R.3
  • 11
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • Brenner SE, Chothia C, Hubbard TJP. Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. Proc Natl Acad Sci USA 1998;95:6073-6078.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 6073-6078
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.P.3
  • 12
    • 0027479161 scopus 로고
    • OB(oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for non-homologous sequences
    • Murzin AG. OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J 1993;12(3):861-867.
    • (1993) EMBO J , vol.12 , Issue.3 , pp. 861-867
    • Murzin, A.G.1
  • 13
    • 0030776390 scopus 로고    scopus 로고
    • Identifying distantly related protein sequences
    • Pearson WR. Identifying distantly related protein sequences. Comp Appl Biosci 1997;13(4):325-332.
    • (1997) Comp Appl Biosci , vol.13 , Issue.4 , pp. 325-332
    • Pearson, W.R.1
  • 14
    • 0029933671 scopus 로고    scopus 로고
    • Effective protein sequence comparison
    • Pearson WR. Effective protein sequence comparison. Methods Enzymol 1996;266:227-258.
    • (1996) Methods Enzymol , vol.266 , pp. 227-258
    • Pearson, W.R.1
  • 15
    • 0026817136 scopus 로고
    • Reconstructing history with amino acid sequences
    • Doolittle RF. Reconstructing history with amino acid sequences. Protein Sci 1992;1:191-200.
    • (1992) Protein Sci , vol.1 , pp. 191-200
    • Doolittle, R.F.1
  • 16
    • 0026656815 scopus 로고
    • Exhaustive matching of the entire protein sequence database
    • Gonnet GH, Cohen MA, Benner SA. Exhaustive matching of the entire protein sequence database. Science 1992;256:1443-1445.
    • (1992) Science , vol.256 , pp. 1443-1445
    • Gonnet, G.H.1    Cohen, M.A.2    Benner, S.A.3
  • 18
    • 0032919372 scopus 로고    scopus 로고
    • Recent improvements of the ProDom database of protein domain families
    • Corpet F, Gouzy J, Kahn D. Recent improvements of the ProDom database of protein domain families. Nucleic Acids Res 1999;27: 263-267.
    • (1999) Nucleic Acids Res , vol.27 , pp. 263-267
    • Corpet, F.1    Gouzy, J.2    Kahn, D.3
  • 19
    • 0029074668 scopus 로고
    • A comprehensive representation of extensive similarity linkage between large numbers of proteins
    • Watanabe H, Otsuka J. A comprehensive representation of extensive similarity linkage between large numbers of proteins. Comp Appl Biosci 1995;11(2):159-166.
    • (1995) Comp Appl Biosci , vol.11 , Issue.2 , pp. 159-166
    • Watanabe, H.1    Otsuka, J.2
  • 22
    • 0031576361 scopus 로고    scopus 로고
    • Intermediate sequences increase the detection of homology between sequences
    • Park J, Teichmann SA, Hubbard T, Chothia C. Intermediate sequences increase the detection of homology between sequences. J Mol Biol 1997;273:349-354.
    • (1997) J Mol Biol , vol.273 , pp. 349-354
    • Park, J.1    Teichmann, S.A.2    Hubbard, T.3    Chothia, C.4
  • 27
    • 0031876699 scopus 로고    scopus 로고
    • Automated protein sequence database classification. I. Integration of copositional similarity search, local similarity search and multiple sequence alignment. II. Delineation of domain boundaries from sequence similarity
    • Gracy J, Argos P. Automated protein sequence database classification. I. Integration of copositional similarity search, local similarity search and multiple sequence alignment. II. Delineation of domain boundaries from sequence similarity. Bioinformatics 1998; 14(2):164-187.
    • (1998) Bioinformatics , vol.14 , Issue.2 , pp. 164-187
    • Gracy, J.1    Argos, P.2
  • 28
    • 0032919370 scopus 로고    scopus 로고
    • SMART: Identification and annotation of domains from signalling and extracellular protein sequences
    • Ponting CP, Schultz J, Milpetz F, Bork P. SMART: identification and annotation of domains from signalling and extracellular protein sequences. Nucleic Acids Res 1999;27:229-232.
    • (1999) Nucleic Acids Res , vol.27 , pp. 229-232
    • Ponting, C.P.1    Schultz, J.2    Milpetz, F.3    Bork, P.4
  • 29
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Tatusov RL, Eugene VK, David JL. A genomic perspective on protein families. Science 1997;278:631-637.
    • (1997) Science , vol.278 , pp. 631-637
    • Tatusov, R.L.1    Eugene, V.K.2    David, J.L.3
  • 30
    • 0029934458 scopus 로고    scopus 로고
    • Superfamily classification in PIR-international protein sequence database
    • Barker WC, Pfeiffer F, George DG. Superfamily classification in PIR-international protein sequence database. Methods Enzymol 1996;266:59-71.
    • (1996) Methods Enzymol , vol.266 , pp. 59-71
    • Barker, W.C.1    Pfeiffer, F.2    George, D.G.3
  • 31
    • 0031876711 scopus 로고    scopus 로고
    • A set-theoretic approach to database searching and clustering
    • Krause A, Vingron M. A set-theoretic approach to database searching and clustering. Bioinformatics 1998;14(5):430-438.
    • (1998) Bioinformatics , vol.14 , Issue.5 , pp. 430-438
    • Krause, A.1    Vingron, M.2
  • 32
    • 0025826412 scopus 로고
    • A new family of powerful multivariate statistical sequence analysis techniques
    • van Heel M. A new family of powerful multivariate statistical sequence analysis techniques. J Mol Biol 1991;220:877-887.
    • (1991) J Mol Biol , vol.220 , pp. 877-887
    • Van Heel, M.1
  • 33
    • 0028279918 scopus 로고
    • Self-organized neural maps of human protein sequences
    • Ferran EA, Pflugfelder B, Ferrara P. Self-organized neural maps of human protein sequences. Protein Sci 1994;3:507-521.
    • (1994) Protein Sci , vol.3 , pp. 507-521
    • Ferran, E.A.1    Pflugfelder, B.2    Ferrara, P.3
  • 34
    • 0029115481 scopus 로고
    • A sequence property approach to searching protein database
    • Hobohm U, Sander C. A sequence property approach to searching protein database. J Mol Biol 1995;251:390-399.
    • (1995) J Mol Biol , vol.251 , pp. 390-399
    • Hobohm, U.1    Sander, C.2
  • 35
    • 0026562263 scopus 로고
    • The SWISS-PROT protein sequence data bank
    • Bairoch A, Boeckman B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res 1992;20:2019-2022.
    • (1992) Nucleic Acids Res , vol.20 , pp. 2019-2022
    • Bairoch, A.1    Boeckman, B.2
  • 37
    • 0031547967 scopus 로고    scopus 로고
    • Global self organization of all known protein sequences reveals inherent biological signatures
    • Linial M, Linial N, Tishby N, Yona G. Global self organization of all known protein sequences reveals inherent biological signatures. J Mol Biol 1997;268:539-556.
    • (1997) J Mol Biol , vol.268 , pp. 539-556
    • Linial, M.1    Linial, N.2    Tishby, N.3    Yona, G.4
  • 39
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S, Henikoff JG. Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992;89:10915-10919.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 41
    • 0032512799 scopus 로고    scopus 로고
    • Empirical statistical estimates for sequence similarity searches
    • Pearson WR. Empirical statistical estimates for sequence similarity searches. J Mol Biol 1998;276:71-84.
    • (1998) J Mol Biol , vol.276 , pp. 71-84
    • Pearson, W.R.1
  • 42
    • 0029006770 scopus 로고
    • Comparison of methods for searching protein sequence databases
    • Pearson WR. Comparison of methods for searching protein sequence databases. Protein Sci 1995;4:1145-1160.
    • (1995) Protein Sci , vol.4 , pp. 1145-1160
    • Pearson, W.R.1
  • 43
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul SF. Amino acid substitution matrices from an information theoretic perspective. J Mol Biol 1991;219:555-565.
    • (1991) J Mol Biol , vol.219 , pp. 555-565
    • Altschul, S.F.1
  • 44
    • 0025259313 scopus 로고
    • Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes
    • Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc Natl Acad Sci USA 1990;87:2264-2268.
    • (1990) Proc Natl Acad Sci USA , vol.87 , pp. 2264-2268
    • Karlin, S.1    Altschul, S.F.2
  • 45
    • 0001514262 scopus 로고
    • Statistics of local complexity in amino acid sequences and sequence databases
    • Wootton JC, Federhen S. Statistics of local complexity in amino acid sequences and sequence databases. Comp Chem 1993;17:149-163.
    • (1993) Comp Chem , vol.17 , pp. 149-163
    • Wootton, J.C.1    Federhen, S.2
  • 46
    • 0027122748 scopus 로고
    • One thousand families for the molecular biologist
    • Chothia C. One thousand families for the molecular biologist. Nature 1992;357:543-544.
    • (1992) Nature , vol.357 , pp. 543-544
    • Chothia, C.1
  • 48
    • 0029857657 scopus 로고    scopus 로고
    • How many fold types of protein are there in nature?
    • Wang Z. How many fold types of protein are there in nature? Proteins 1996;26:186-191.
    • (1996) Proteins , vol.26 , pp. 186-191
    • Wang, Z.1
  • 49
    • 0030983386 scopus 로고    scopus 로고
    • Population statistics of protein structures: Lessons from structural classifications
    • Brenner SE, Chothia C, Hubbard TJP. Population statistics of protein structures: lessons from structural classifications. Curr Opin Struct Biol 1997;7:369-376.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 369-376
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.P.3
  • 51
    • 0028239912 scopus 로고
    • GTPase: Multifunctional molecular switches regulating vesicular traffic
    • Nuoffer C, Balch W. GTPase: multifunctional molecular switches regulating vesicular traffic. Annu Rev Biochem 1994;63:949-990.
    • (1994) Annu Rev Biochem , vol.63 , pp. 949-990
    • Nuoffer, C.1    Balch, W.2
  • 52
    • 0025260565 scopus 로고
    • The ras superfamily of small GTP-binding proteins
    • Downward J. The ras superfamily of small GTP-binding proteins. Trends Biochem Sci 1990;15:469-472.
    • (1990) Trends Biochem Sci , vol.15 , pp. 469-472
    • Downward, J.1
  • 53
    • 0028361540 scopus 로고
    • Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains
    • Harpez Y, Chothia C. Many of the immunoglobulin superfamily domains in cell adhesion molecules and surface receptors belong to a new structural set which is close to that containing variable domains. J Mol Biol 1994;238:528-539.
    • (1994) J Mol Biol , vol.238 , pp. 528-539
    • Harpez, Y.1    Chothia, C.2
  • 54
    • 0031565975 scopus 로고    scopus 로고
    • Sequence profiles of immunoglobulin and immunoglobulin-like domains
    • Smith DK, Xue H. Sequence profiles of immunoglobulin and immunoglobulin-like domains. J Mol Biol 1997;274:530-545.
    • (1997) J Mol Biol , vol.274 , pp. 530-545
    • Smith, D.K.1    Xue, H.2


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