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Volumn 8, Issue , 2007, Pages

A topological algorithm for identification of structural domains of proteins

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATE DESCRIPTIONS; COMPARATIVE SEQUENCE ANALYSIS; ORGANIZATIONAL PRINCIPLES; SECONDARY STRUCTURE ELEMENTS; SIGNIFICANT DETERIORATIONS; THREE-DIMENSIONAL STRUCTURE; TOPOLOGICAL ALGORITHMS; TOPOLOGICAL INFORMATION;

EID: 34547667016     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-237     Document Type: Article
Times cited : (22)

References (34)
  • 1
    • 31144467558 scopus 로고    scopus 로고
    • The Impact of Structural Genomics: Expectations and Outcomes
    • 10.1126/science.1121018 16424331
    • Chandonia JM Brenner SE The Impact of Structural Genomics: Expectations and Outcomes Science 2006 311 5759 347-351 10.1126/science.1121018 16424331
    • (2006) Science , vol.311 , Issue.5759 , pp. 347-351
    • Chandonia, J.M.1    Brenner, S.E.2
  • 2
    • 0013971370 scopus 로고
    • The three-dimensional structure of an enzyme molecule
    • 5978599
    • Phillips DC The three-dimensional structure of an enzyme molecule Sci Am 1966 215 78-90 5978599
    • (1966) Sci Am , vol.215 , pp. 78-90
    • Phillips, D.C.1
  • 3
    • 0346494941 scopus 로고    scopus 로고
    • SCOP database in 2004: Refinements integrate structure and sequence family data
    • 308773 14681400 10.1093/nar/gkh039
    • Andreeva A Howorth D Brenner SE Hubbard TJ Chothia C Murzin AG SCOP database in 2004: Refinements integrate structure and sequence family data Nucleic Acids Res 2004 32 D226-229 308773 14681400 10.1093/nar/ gkh039
    • (2004) Nucleic Acids Res , vol.32
    • Andreeva, A.1    Howorth, D.2    Brenner, S.E.3    Hubbard, T.J.4    Chothia, C.5    Murzin, A.G.6
  • 4
    • 13444282474 scopus 로고    scopus 로고
    • InterPro, progress and status in 2005
    • 540060 15608177 10.1093/nar/gki106
    • Mulder N Jea InterPro, progress and status in 2005 Nucleic Acids Res 2005 33 D201-205 540060 15608177 10.1093/nar/gki106
    • (2005) Nucleic Acids Res , vol.33
    • Mulder, N.J.1
  • 5
    • 0015597839 scopus 로고
    • Nucleation, rapid folding, and globular intrachain regions in proteins
    • 433338 4351801 10.1073/pnas.70.3.697
    • Wetlaufer D Nucleation, rapid folding, and globular intrachain regions in proteins Proc Natl Acad Sci 1973 70 697-701 433338 4351801 10.1073/ pnas.70.3.697
    • (1973) Proc Natl Acad Sci , vol.70 , pp. 697-701
    • Wetlaufer, D.1
  • 6
    • 0016255253 scopus 로고
    • Recognition of structural domains in globular proteins
    • 10.1016/0022-2836(74)90136-3 4365123
    • Rossmann MG Liljas A Recognition of structural domains in globular proteins J Mol Biol 1974 85 177-181 10.1016/0022-2836(74)90136-3 4365123
    • (1974) J Mol Biol , vol.85 , pp. 177-181
    • Rossmann, M.G.1    Liljas, A.2
  • 7
    • 0029006062 scopus 로고
    • The multiplicity of domains in proteins
    • 10.1146/annurev.bi.64.070195.001443 7574483
    • Doolittle RF The multiplicity of domains in proteins Annu Rev Biochem 1995 64 287-314 10.1146/annurev.bi.64.070195.001443 7574483
    • (1995) Annu Rev Biochem , vol.64 , pp. 287-314
    • Doolittle, R.F.1
  • 8
    • 2442622545 scopus 로고    scopus 로고
    • Toward consistent assignment of structural domains in proteins
    • 10.1016/j.jmb.2004.03.053 15147847
    • Veretnik S Bourne PE Alexandrov NN Shindyalov IN Toward consistent assignment of structural domains in proteins J Mol Biol 2004 339 647-678 10.1016/j.jmb.2004.03.053 15147847
    • (2004) J Mol Biol , vol.339 , pp. 647-678
    • Veretnik, S.1    Bourne, P.E.2    Alexandrov, N.N.3    Shindyalov, I.N.4
  • 9
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • AJ E, S VD, CA O. 101833 11917018 10.1093/nar/30.7.1575
    • AJ E S VD CA O An efficient algorithm for large-scale detection of protein families Nucleic Acids Res 2002 30 7 1575-84 101833 11917018 10.1093/nar/30.7.1575
    • (2002) Nucleic Acids Res , vol.30 , Issue.7 , pp. 1575-1584
  • 10
    • 0036306348 scopus 로고    scopus 로고
    • SnapDRAGON: A method to delineate protein structural domains from sequence data
    • RA G, J H 10.1006/jmbi.2001.5387 11866536
    • RA G J H SnapDRAGON: A method to delineate protein structural domains from sequence data J Mol Biol 2002 316 3 839-51 10.1006/jmbi.2001.5387 11866536
    • (2002) J Mol Biol , vol.316 , Issue.3 , pp. 839-851
  • 11
    • 19544382558 scopus 로고    scopus 로고
    • Prediction of protein interdomain linker regions by a hidden Markov model
    • K B BK M CG E. 10.1093/bioinformatics/bti363 15746283
    • K B BK M CG E Prediction of protein interdomain linker regions by a hidden Markov model Bioinformatics 2005 21 10 2264-70 10.1093/ bioinformatics/bti363 15746283
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2264-2270
  • 12
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • 10.1006/jmbi.1995.0159 7723011
    • 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 10.1006/jmbi.1995.0159 7723011
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 13
    • 0030777303 scopus 로고    scopus 로고
    • CATH-A Hierarchic Classification of Protein Domain Structures
    • 10.1016/S0969-2126(97)00260-8 9309224
    • Orengo C Michie A Jones S Jones D Swindells M Thornton J CATH-A Hierarchic Classification of Protein Domain Structures Structure 1997 5 8 1093-1108 10.1016/S0969-2126(97)00260-8 9309224
    • (1997) Structure , vol.5 , Issue.8 , pp. 1093-1108
    • Orengo, C.1    Michie, A.2    Jones, S.3    Jones, D.4    Swindells, M.5    Thornton, J.6
  • 14
    • 33746338567 scopus 로고    scopus 로고
    • Partitioning protein structures into domains: Why is it so difficult?
    • 10.1016/j.jmb.2006.05.060 16863650
    • Holland TA Veretnik S Shindyalov IN Bourne PE Partitioning protein structures into domains: Why is it so difficult? J Mol Biol 2006 361 562-590 10.1016/j.jmb.2006.05.060 16863650
    • (2006) J Mol Biol , vol.361 , pp. 562-590
    • Holland, T.A.1    Veretnik, S.2    Shindyalov, I.N.3    Bourne, P.E.4
  • 15
    • 0032951163 scopus 로고    scopus 로고
    • Protein structural domain identification
    • 10.1093/protein/12.3.203 10235621
    • Taylor WR Protein structural domain identification Protein Eng 1999 12 3 203-216 10.1093/protein/12.3.203 10235621
    • (1999) Protein Eng , vol.12 , Issue.3 , pp. 203-216
    • Taylor, W.R.1
  • 16
    • 84926736518 scopus 로고
    • Some generalized order-disorder transformations
    • Potts RB Some generalized order-disorder transformations Proceedings of the Cambridge Society 1953 48 106-109
    • (1953) Proceedings of the Cambridge Society , vol.48 , pp. 106-109
    • Potts, R.B.1
  • 17
    • 0000521616 scopus 로고    scopus 로고
    • Superparamagnetic Clustering of Data
    • 10.1103/PhysRevLett.76.3251 10060920
    • Blatt M Wiesman S Domany E Superparamagnetic Clustering of Data Phys Rev Lett 1996 76 3251 10.1103/PhysRevLett.76.3251 10060920
    • (1996) Phys Rev Lett , vol.76 , pp. 3251
    • Blatt, M.1    Wiesman, S.2    Domany, E.3
  • 18
    • 0000902522 scopus 로고    scopus 로고
    • Data Clustering using a model granular magnet
    • 10.1162/neco.1997.9.8.1805
    • Blatt M Wiesman S Domany E Data Clustering using a model granular magnet Neural Computation 1997 9 1805-1842 10.1162/neco.1997.9.8.1805
    • (1997) Neural Computation , vol.9 , pp. 1805-1842
    • Blatt, M.1    Wiesman, S.2    Domany, E.3
  • 19
    • 0034491038 scopus 로고    scopus 로고
    • Protein domain decomposition using a graph-theoretic approach
    • 10.1093/bioinformatics/16.12.1091 11159328
    • Xu Y Xu D Gabow HN Protein domain decomposition using a graph-theoretic approach Bioinformatics 2000 16 12 1091-1104 10.1093/bioinformatics/ 16.12.1091 11159328
    • (2000) Bioinformatics , vol.16 , Issue.12 , pp. 1091-1104
    • Xu, Y.1    Xu, D.2    Gabow, H.N.3
  • 20
    • 0037324306 scopus 로고    scopus 로고
    • Improving the performance of DomainParser for structural domain partition using neural network
    • 149209 12560490 10.1093/nar/gkg189 D K
    • Guo Jt Xu D D K Xu Y Improving the performance of DomainParser for structural domain partition using neural network Nucl Acids Res 2003 31 3 944-952 149209 12560490 10.1093/nar/gkg189
    • (2003) Nucl Acids Res , vol.31 , Issue.3 , pp. 944-952
    • Guo, Jt.1    Xu, D.2    Xu, Y.3
  • 25
    • 0031889752 scopus 로고    scopus 로고
    • Domain assignment for protein structures using a consensus approach: Characterization and analysis
    • 9521098
    • Jones S Steward M Michie A Swindells MB Orengo C Thornton JM Domain assignment for protein structures using a consensus approach: characterization and analysis Protein Sci 1998 7 233-242 9521098
    • (1998) Protein Sci , vol.7 , pp. 233-242
    • Jones, S.1    Steward, M.2    Michie, A.3    Swindells, M.B.4    Orengo, C.5    Thornton, J.M.6
  • 26
    • 0001720243 scopus 로고    scopus 로고
    • Symmetries in proteins: A knot theory approach
    • 10.1063/1.471328
    • Chen SJ Dill KA Symmetries in proteins: A knot theory approach J Chem Phys 1996 104 15 5964-5973 10.1063/1.471328
    • (1996) J Chem Phys , vol.104 , Issue.15 , pp. 5964-5973
    • Chen, S.J.1    Dill, K.A.2
  • 27
    • 23844494717 scopus 로고    scopus 로고
    • Protein Similarity from Knot Theory: Geometric Convolution and Line Weavings
    • 10.1089/cmb.2005.12.609 16108707
    • Erdmann MA Protein Similarity from Knot Theory: Geometric Convolution and Line Weavings Journal of Computational Biology 2005 12 6 609-637 10.1089/cmb.2005.12.609 16108707
    • (2005) Journal of Computational Biology , vol.12 , Issue.6 , pp. 609-637
    • Erdmann, M.A.1
  • 28
    • 0037422619 scopus 로고    scopus 로고
    • Automatic classification of protein structure by using Gauss integrals
    • 140900 12506205 10.1073/pnas.2636460100
    • Rogen P Fain B Automatic classification of protein structure by using Gauss integrals Proc Natl Acad Sci USA 2003 100 119124 140900 12506205 10.1073/pnas.2636460100
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 119-124
    • Rogen, P.1    Fain, B.2
  • 29
    • 34547671421 scopus 로고    scopus 로고
    • Algorithmic Computation of Knot Polynomials of Secondary Structure Elements of Proteins
    • 10.1089/cmb.2006.13.1503 17061925
    • Emmert-Streib F Algorithmic Computation of Knot Polynomials of Secondary Structure Elements of Proteins Journal of Computational Biology 2006 13 8 1503-1512 10.1089/cmb.2006.13.1503 17061925
    • (2006) Journal of Computational Biology , vol.13 , Issue.8 , pp. 1503-1512
    • Emmert-Streib, F.1
  • 31
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features
    • 10.1002/bip.360221211 6667333
    • Kabsch W Sander C Dictionary of protein secondary structure: Pattern recognition of hydrogen bonded and geometrical features Biopolymers 1983 22 2577-2637 10.1002/bip.360221211 6667333
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 32
    • 0029619259 scopus 로고
    • Knowledge-based protein secondary structure assignment
    • 10.1002/prot.340230412 8749853
    • Frishman D Argos P Knowledge-based protein secondary structure assignment Proteins 1995 23 566-579 10.1002/prot.340230412 8749853
    • (1995) Proteins , vol.23 , pp. 566-579
    • Frishman, D.1    Argos, P.2
  • 33
    • 0018782641 scopus 로고
    • Hierarchic organization of domains in globular proteins
    • 10.1016/0022-2836(79)90363-2 537072
    • Rose GD Hierarchic organization of domains in globular proteins J Mol Biol 1979 134 3 447-470 10.1016/0022-2836(79)90363-2 537072
    • (1979) J Mol Biol , vol.134 , pp. 447-470
    • Rose, G.D.1
  • 34
    • 0028943588 scopus 로고
    • Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions
    • 7663343
    • Siddiqui AS Barton GJ Continuous and discontinuous domains: An algorithm for the automatic generation of reliable protein domain definitions Protein Science 1995 4 872-884 7663343
    • (1995) Protein Science , vol.4 , pp. 872-884
    • Siddiqui, A.S.1    Barton, G.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.