메뉴 건너뛰기




Volumn 77, Issue 2, 2009, Pages 448-453

Predicting structurally conserved contacts for homologous proteins using sequence conservation filters

Author keywords

Contact prediction; G protein coupled receptors; Intramolecular contacts; Sequence conservation; Structural homology; Template based structure prediction

Indexed keywords

G PROTEIN COUPLED RECEPTOR;

EID: 84860183160     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22456     Document Type: Article
Times cited : (8)

References (30)
  • 5
    • 0038024615 scopus 로고    scopus 로고
    • The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
    • Fredriksson R, Lagerstrom MC, Lundin LG, Schioth HB. The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 2003;63:1256-1272.
    • (2003) Mol Pharmacol , vol.63 , pp. 1256-1272
    • Fredriksson, R.1    Lagerstrom, M.C.2    Lundin, L.G.3    Schioth, H.B.4
  • 6
    • 33645792604 scopus 로고    scopus 로고
    • Physically realistic homology models built with ROSETTA can be more accurate than their templates
    • Misura KM, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci USA 2006;103:5361-5366.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5361-5366
    • Misura, K.M.1    Chivian, D.2    Rohl, C.A.3    Kim, D.E.4    Baker, D.5
  • 8
    • 34248549547 scopus 로고    scopus 로고
    • Can molecular dynamics simulations provide high-resolution refinement of protein structure?
    • Chen J, Brooks CL, III. Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 2007;67:922-930.
    • (2007) Proteins , vol.67 , pp. 922-930
    • Chen, J.1    Brooks III, C.L.2
  • 9
    • 0031575423 scopus 로고    scopus 로고
    • MONSSTER: A method for folding globular proteins with a small number of distance restraints
    • DOI 10.1006/jmbi.1996.0720
    • Skolnick J, Kolinski A, Ortiz AR. MONSSTER: a method for folding globular proteins with a small number of distance restraints. J Mol Biol 1997;265:217-241. (Pubitemid 27110659)
    • (1997) Journal of Molecular Biology , vol.265 , Issue.2 , pp. 217-241
    • Skolnick, J.1    Kolinski, A.2    Ortiz, A.R.3
  • 10
    • 41349114023 scopus 로고    scopus 로고
    • A comprehensive assessment of sequence-based and template-based methods for protein contact prediction
    • Wu S, Zhang Y. A comprehensive assessment of sequence-based and template-based methods for protein contact prediction. Bioinformatics 2008;24:924-931.
    • (2008) Bioinformatics , vol.24 , pp. 924-931
    • Wu, S.1    Zhang, Y.2
  • 13
    • 0033047710 scopus 로고    scopus 로고
    • A neural network based predictor of residue contacts in proteins
    • Fariselli P, Casadio R. A neural network based predictor of residue contacts in proteins. Protein Eng 1999;12:15-21. (Pubitemid 29050537)
    • (1999) Protein Engineering , vol.12 , Issue.1 , pp. 15-21
    • Fariselli, P.1    Casadio, R.2
  • 15
    • 0024373407 scopus 로고
    • Conservation of residue interactions in a family of Ca-binding proteins
    • Godzik A, Sander C. Conservation of residue interactions in a family of Ca-binding proteins. Protein Eng 1989;2:589-596. (Pubitemid 19212141)
    • (1989) Protein Engineering , vol.2 , Issue.8 , pp. 589-596
    • Godzik, A.1    Sander, C.2
  • 16
    • 23144448512 scopus 로고    scopus 로고
    • ConSurf 2005: The projection of evolutionary conservation scores of residues on protein structures
    • DOI 10.1093/nar/gki370
    • Landau M, Mayrose I, Rosenberg Y, Glaser F, Martz E, Pupko T, Ben-Tal N. ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. Nucleic Acids Res 2005;33(Web Server issue):W299-W302. (Pubitemid 44529930)
    • (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS
    • Landau, M.1    Mayrose, I.2    Rosenberg, Y.3    Glaser, F.4    Martz, E.5    Pupko, T.6    Ben-Tal, N.7
  • 17
    • 0042622381 scopus 로고    scopus 로고
    • LGA: A method for finding 3D similarities in protein structures
    • DOI 10.1093/nar/gkg571
    • Zemla A. LGA: A method for finding 3D similarities in protein structures. Nucleic Acids Res 2003;31:3370-3374. (Pubitemid 37442162)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3370-3374
    • Zemla, A.1
  • 18
    • 1942423619 scopus 로고    scopus 로고
    • MMTSB Tool Set: Enhanced sampling and multiscale modeling methods for applications in structural biology
    • DOI 10.1016/j.jmgm.2003.12.005, PII S1093326303001943
    • Feig M, Karanicolas J, Brooks CL, III. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 2004;22:377-395. (Pubitemid 38510304)
    • (2004) Journal of Molecular Graphics and Modelling , vol.22 , Issue.5 , pp. 377-395
    • Feig, M.1    Karanicolas, J.2    Brooks III, C.L.3
  • 19
    • 0035866002 scopus 로고    scopus 로고
    • Defrosting the frozen approximation: PROSPECTOR - A new approach to threading
    • DOI 10.1002/1097-0134(20010215)42:3<319::AID-PROT30>3.0.CO;2-A
    • Skolnick J, Kihara D. Defrosting the frozen approximation: PROSPECTOR - a new approach to threading. Proteins 2001;42:319-331. (Pubitemid 32107757)
    • (2001) Proteins: Structure, Function and Genetics , vol.42 , Issue.3 , pp. 319-331
    • Skolnick, J.1    Kihara, D.2
  • 21
    • 2942589291 scopus 로고    scopus 로고
    • The linked conservation of structure and function in a family of high diversity: The monomeric cupredoxins
    • DOI 10.1016/j.str.2004.03.029, PII S0969212604001583
    • Gough J, Chothia C. The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins. Structure 2004;12:917-925. (Pubitemid 38748765)
    • (2004) Structure , vol.12 , Issue.6 , pp. 917-925
    • Gough, J.1    Chothia, C.2
  • 22
    • 0037219686 scopus 로고    scopus 로고
    • Evolutionarily conserved networks of residues mediate allosteric communication in proteins
    • DOI 10.1038/nsb881
    • Suel GM, Lockless SW, Wall MA, Ranganathan R. Evolutionarily conserved networks of residues mediate allosteric communication in proteins. Nat Struct Biol 2003;10:59-69. (Pubitemid 36034178)
    • (2003) Nature Structural Biology , vol.10 , Issue.1 , pp. 59-69
    • Suel, G.M.1    Lockless, S.W.2    Wall, M.A.3    Ranganathan, R.4
  • 23
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences
    • DOI 10.1093/bioinformatics/btl158
    • Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006;22:1658-1659. (Pubitemid 43985301)
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 24
    • 0036681416 scopus 로고    scopus 로고
    • Scoring residue conservation
    • Valdar WS. Scoring residue conservation. Proteins 2002;48:227-241.
    • (2002) Proteins , vol.48 , pp. 227-241
    • Valdar, W.S.1
  • 26
    • 0025277191 scopus 로고
    • The classification and origins of protein folding patterns
    • Chothia C, Finkelstein AV. The classification and origins of protein folding patterns. Annu Rev Biochem 1990;59:1007-1039. (Pubitemid 20207030)
    • (1990) Annual Review of Biochemistry , vol.59 , pp. 1007-1039
    • Chothia, C.1    Finkelstein, A.V.2
  • 28
    • 3042681902 scopus 로고    scopus 로고
    • ConSeq: The identification of functionally and structurally important residues in protein sequences
    • DOI 10.1093/bioinformatics/bth070
    • Berezin C, Glaser F, Rosenberg J, Paz I, Pupko T, Fariselli P, Casadio R, Ben-Tal N. ConSeq: the identification of functionally and structurally important residues in protein sequences. Bioinformatics 2004;20:1322-1324. (Pubitemid 38807587)
    • (2004) Bioinformatics , vol.20 , Issue.8 , pp. 1322-1324
    • Berezin, C.1    Glaser, F.2    Rosenberg, J.3    Paz, I.4    Pupko, T.5    Fariselli, P.6    Casadio, R.7    Ben-Tal, N.8
  • 30
    • 4143110064 scopus 로고    scopus 로고
    • Application of sparse NMR restraints to large-scale protein structure prediction
    • DOI 10.1529/biophysj.104.044750
    • Li W, Zhang Y, Skolnick J. Application of sparse NMR restraints to large-scale protein structure prediction. Biophys J 2004;87:1241-1248. (Pubitemid 39095100)
    • (2004) Biophysical Journal , vol.87 , Issue.2 , pp. 1241-1248
    • Li, W.1    Zhang, Y.2    Skolnick, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.