메뉴 건너뛰기




Volumn 43, Issue 2, 2010, Pages 257-267

A similarity network approach for the analysis and comparison of protein sequence/structure sets

Author keywords

Alignment; Betweenness; Evolution; Hub; Network; Protein sequence; Protein structure; Sequence derived features; Small World Network

Indexed keywords

BETWEENNESS; HUB NETWORKS; PROTEIN SEQUENCE; PROTEIN SEQUENCES; PROTEIN STRUCTURES; SMALL WORLD NETWORKS;

EID: 77949270793     PISSN: 15320464     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbi.2010.01.005     Document Type: Article
Times cited : (14)

References (31)
  • 1
    • 0032482432 scopus 로고    scopus 로고
    • Collective dynamics of small-world networks
    • Watts D.J., and Strogatz S.H. Collective dynamics of small-world networks. Nature 393 (1998) 440-442
    • (1998) Nature , vol.393 , pp. 440-442
    • Watts, D.J.1    Strogatz, S.H.2
  • 2
    • 0035826155 scopus 로고    scopus 로고
    • Exploring complex networks
    • Strogatz S.H. Exploring complex networks. Nature 410 (2001) 268-276
    • (2001) Nature , vol.410 , pp. 268-276
    • Strogatz, S.H.1
  • 4
    • 0242720597 scopus 로고    scopus 로고
    • Uncovering network systems within protein structures
    • Greene L.H., and Higman V.A. Uncovering network systems within protein structures. J Mol Biol 334 (2003) 781-791
    • (2003) J Mol Biol , vol.334 , pp. 781-791
    • Greene, L.H.1    Higman, V.A.2
  • 5
    • 41349118690 scopus 로고    scopus 로고
    • Small-world view of the amino acids that play a key role in protein folding
    • Vendruscolo M., Dokholyan N.V., Paci E., and Karplus M. Small-world view of the amino acids that play a key role in protein folding. Phys Rev E 65 (2002) id. 061910
    • (2002) Phys Rev E , vol.65
    • Vendruscolo, M.1    Dokholyan, N.V.2    Paci, E.3    Karplus, M.4
  • 6
    • 8544221118 scopus 로고    scopus 로고
    • Network analysis of protein structures identifies functional residues
    • Amitai G., et al. Network analysis of protein structures identifies functional residues. J Mol Biol 344 (2004) 1135-1144
    • (2004) J Mol Biol , vol.344 , pp. 1135-1144
    • Amitai, G.1
  • 7
    • 0037173002 scopus 로고    scopus 로고
    • Topological determinants of protein folding
    • Dokholyan N.V., et al. Topological determinants of protein folding. Proc Natl Acad Sci USA 99 (2002) 8637-8641
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 8637-8641
    • Dokholyan, N.V.1
  • 8
    • 33745596822 scopus 로고    scopus 로고
    • Integrating multi-attribute similarity networks for robust representation of the protein space
    • Camoglu O., Can T., and Singh A.K. Integrating multi-attribute similarity networks for robust representation of the protein space. Bioinformatics 22 (2006) 1585-1592
    • (2006) Bioinformatics , vol.22 , pp. 1585-1592
    • Camoglu, O.1    Can, T.2    Singh, A.K.3
  • 9
    • 0037195119 scopus 로고    scopus 로고
    • Expanding protein universe and its origin from the biological Big Bang
    • Dokholyan N.V., Shakhnovich B., and Shakhnovich E.I. Expanding protein universe and its origin from the biological Big Bang. Proc Natl Acad Sci USA 99 (2002) 14132-14136
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 14132-14136
    • Dokholyan, N.V.1    Shakhnovich, B.2    Shakhnovich, E.I.3
  • 10
    • 24344474827 scopus 로고    scopus 로고
    • A graph spectral analysis of the structural similarity network of protein chains
    • Krishnadev O., Brinda K.V., and Vishveshwara S. A graph spectral analysis of the structural similarity network of protein chains. Proteins Struct Funct Bioinf 61 (2005) 152-163
    • (2005) Proteins Struct Funct Bioinf , vol.61 , pp. 152-163
    • Krishnadev, O.1    Brinda, K.V.2    Vishveshwara, S.3
  • 11
    • 31744442227 scopus 로고    scopus 로고
    • The architectonic fold similarity network in protein fold space
    • Sun Z.B., Zou X.W., Guan W., and Jin Z.Z. The architectonic fold similarity network in protein fold space. Eur Phys J B 49 (2006) 127-134
    • (2006) Eur Phys J B , vol.49 , pp. 127-134
    • Sun, Z.B.1    Zou, X.W.2    Guan, W.3    Jin, Z.Z.4
  • 13
    • 0035014847 scopus 로고    scopus 로고
    • Multi-class protein fold recognition using support vector machines and neural networks
    • Ding C.H.Q., and Dubchak I. Multi-class protein fold recognition using support vector machines and neural networks. Bioinformatics 7 (2001) 349-358
    • (2001) Bioinformatics , vol.7 , pp. 349-358
    • Ding, C.H.Q.1    Dubchak, I.2
  • 16
    • 0028205447 scopus 로고
    • Enlarged representative set of protein structures
    • Hobohm U., and Sander C. Enlarged representative set of protein structures. Protein Sci 3 (1994) 522-524
    • (1994) Protein Sci , vol.3 , pp. 522-524
    • Hobohm, U.1    Sander, C.2
  • 17
    • 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. 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
  • 18
    • 0033954256 scopus 로고    scopus 로고
    • The protein data bank
    • Berman H.M., et al. The protein data bank. Nucleic Acids Res 28 (2000) 235-242
    • (2000) Nucleic Acids Res , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 19
    • 0033824470 scopus 로고    scopus 로고
    • DaliLite workbench for protein structure comparison
    • Holm L., and Park J. DaliLite workbench for protein structure comparison. Bioinformatics 16 (2000) 566-567
    • (2000) Bioinformatics , vol.16 , pp. 566-567
    • Holm, L.1    Park, J.2
  • 20
    • 4544334185 scopus 로고    scopus 로고
    • F2CS: FSSP to CATH and SCOP prediction server
    • Getz G., Starovolsky A., and Domany E. F2CS: FSSP to CATH and SCOP prediction server. Bioinformatics 20 (2004) 2150-2152
    • (2004) Bioinformatics , vol.20 , pp. 2150-2152
    • Getz, G.1    Starovolsky, A.2    Domany, E.3
  • 21
    • 0029047319 scopus 로고
    • Prediction of protein folding class using global description of amino acid sequence
    • Dubchak I., Muchnik I., Holbrook S.R., and Kim S.H. Prediction of protein folding class using global description of amino acid sequence. Proc Natl Acad Sci USA 92 (1995) 8700-8704
    • (1995) Proc Natl Acad Sci USA , vol.92 , pp. 8700-8704
    • Dubchak, I.1    Muchnik, I.2    Holbrook, S.R.3    Kim, S.H.4
  • 22
    • 2342475726 scopus 로고    scopus 로고
    • Protein ranking: from local to global structure in the protein similarity network
    • Weston J., Elisseeff A., Zhou D., Leslie C.S., and Noble W.S. Protein ranking: from local to global structure in the protein similarity network. Proc Natl Acad Sci USA 101 (2004) 6559-6563
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 6559-6563
    • Weston, J.1    Elisseeff, A.2    Zhou, D.3    Leslie, C.S.4    Noble, W.S.5
  • 23
    • 84865730611 scopus 로고
    • A set of measures of centrality based on betweenness
    • Freeman L.C. A set of measures of centrality based on betweenness. Sociometry 40 (1977) 35-41
    • (1977) Sociometry , vol.40 , pp. 35-41
    • Freeman, L.C.1
  • 24
    • 34247622363 scopus 로고    scopus 로고
    • The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics
    • Yu H., Kim P.M., Sprecher E., Trifonov V., and Gerstein M. The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol 3 (2007) e59
    • (2007) PLoS Comput Biol , vol.3
    • Yu, H.1    Kim, P.M.2    Sprecher, E.3    Trifonov, V.4    Gerstein, M.5
  • 25
    • 0034274870 scopus 로고    scopus 로고
    • An open graph visualization system and its applications to software engineering
    • Gansner E., and North S. An open graph visualization system and its applications to software engineering. Softw Pract Exp 30 (2000) 1203-1233
    • (2000) Softw Pract Exp , vol.30 , pp. 1203-1233
    • Gansner, E.1    North, S.2
  • 26
    • 0038486929 scopus 로고    scopus 로고
    • An evolutionarily structured universe of protein architecture
    • Caetano-Anollés G., and Caetano-Anollés D. An evolutionarily structured universe of protein architecture. Genome Res 13 (2003) 1563-1571
    • (2003) Genome Res , vol.13 , pp. 1563-1571
    • Caetano-Anollés, G.1    Caetano-Anollés, D.2
  • 28
    • 0035783063 scopus 로고    scopus 로고
    • Fold change in evolution of protein structures
    • Grishin N.V. Fold change in evolution of protein structures. J Struct Biol 134 (2001) 167-185
    • (2001) J Struct Biol , vol.134 , pp. 167-185
    • Grishin, N.V.1
  • 29
    • 0027485083 scopus 로고
    • Comparison of conformational characteristics in structurally similar protein pairs
    • Flores T.P., Orengo C.A., Moss D.S., and Thornton T.M. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci 2 (1993) 1811-1826
    • (1993) Protein Sci , vol.2 , pp. 1811-1826
    • Flores, T.P.1    Orengo, C.A.2    Moss, D.S.3    Thornton, T.M.4
  • 30
    • 0037941120 scopus 로고    scopus 로고
    • Scaling law in sizes of protein sequence families: from super-families to orphan genes
    • Unger R., Uliel S., and Havlin S. Scaling law in sizes of protein sequence families: from super-families to orphan genes. Proteins Struct Funct Genet 51 (2003) 569-576
    • (2003) Proteins Struct Funct Genet , vol.51 , pp. 569-576
    • Unger, R.1    Uliel, S.2    Havlin, S.3
  • 31
    • 33747816816 scopus 로고    scopus 로고
    • PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence
    • Li Z.R., et al. PROFEAT: a web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res 34 (2006) W32-W37
    • (2006) Nucleic Acids Res , vol.34
    • Li, Z.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.