메뉴 건너뛰기




Volumn 79, Issue 8, 2011, Pages 2389-2402

Internal organization of large protein families: Relationship between the sequence, structure, and function-based clustering

Author keywords

Comparative modeling; Protein function prediction; Protein structure initiative; Protein structure prediction; Structural genomics

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN FUNCTION; PROTEIN STRUCTURE; STRUCTURAL GENOMICS;

EID: 79960106288     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.23049     Document Type: Article
Times cited : (5)

References (36)
  • 1
    • 85027934053 scopus 로고    scopus 로고
    • The CATH database
    • Knudsen M, Wiuf C. The CATH database. Hum Genomics 2010; 4: 207-212.
    • (2010) Hum Genomics , vol.4 , pp. 207-212
    • Knudsen, M.1    Wiuf, C.2
  • 3
    • 33847069615 scopus 로고    scopus 로고
    • Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization
    • Mirkovic N, Li Z, Parnassa A, Murray D. Strategies for high-throughput comparative modeling: applications to leverage analysis in structural genomics and protein family organization. Proteins 2007; 66: 766-777.
    • (2007) Proteins , vol.66 , pp. 766-777
    • Mirkovic, N.1    Li, Z.2    Parnassa, A.3    Murray, D.4
  • 5
    • 67649795139 scopus 로고    scopus 로고
    • Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure
    • Burra PV, Zhang Y, Godzik A, Stec B. Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure. Proc Natl Acad Sci USA 2009; 106: 10505-10510.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 10505-10510
    • Burra, P.V.1    Zhang, Y.2    Godzik, A.3    Stec, B.4
  • 6
    • 0036314772 scopus 로고    scopus 로고
    • Studying genomes through the aeons: protein families, pseudogenes and proteome evolution
    • Harrison PM, Gerstein M. Studying genomes through the aeons: protein families, pseudogenes and proteome evolution. J Mol Biol 2002; 318: 1155-1174.
    • (2002) J Mol Biol , vol.318 , pp. 1155-1174
    • Harrison, P.M.1    Gerstein, M.2
  • 7
    • 17844379728 scopus 로고    scopus 로고
    • Identification and distribution of protein families in 120 completed genomes using Gene3D
    • Lee D, Grant A, Marsden RL, Orengo C. Identification and distribution of protein families in 120 completed genomes using Gene3D. Proteins 2005; 59: 603-615.
    • (2005) Proteins , vol.59 , pp. 603-615
    • Lee, D.1    Grant, A.2    Marsden, R.L.3    Orengo, C.4
  • 9
    • 33744779891 scopus 로고    scopus 로고
    • Sequence comparison and protein structure prediction
    • Dunbrack RL, Jr. Sequence comparison and protein structure prediction. Curr Opin Struct Biol 2006; 16: 374-384.
    • (2006) Curr Opin Struct Biol , vol.16 , pp. 374-384
    • Dunbrack Jr, R.L.1
  • 10
    • 28444492641 scopus 로고    scopus 로고
    • Computational methods for remote homolog identification
    • Wan XF, Xu D. Computational methods for remote homolog identification. Curr Protein Pept Sci 2005; 6: 527-546.
    • (2005) Curr Protein Pept Sci , vol.6 , pp. 527-546
    • Wan, X.F.1    Xu, D.2
  • 13
    • 0033997036 scopus 로고    scopus 로고
    • Comparison of sequence profiles. Strategies for structural predictions using sequence information
    • Rychlewski L, Jaroszewski L, Li W, Godzik A. Comparison of sequence profiles. Strategies for structural predictions using sequence information. Protein Sci 2000; 9: 232-241.
    • (2000) Protein Sci , vol.9 , pp. 232-241
    • Rychlewski, L.1    Jaroszewski, L.2    Li, W.3    Godzik, A.4
  • 14
    • 0036307493 scopus 로고    scopus 로고
    • Within the twilight zone: a sensitive profile-profile comparison tool based on information theory
    • Yona G, Levitt M. Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. J Mol Biol 2002; 315: 1257-1275.
    • (2002) J Mol Biol , vol.315 , pp. 1257-1275
    • Yona, G.1    Levitt, M.2
  • 15
    • 0037440190 scopus 로고    scopus 로고
    • Finding weak similarities between proteins by sequence profile comparison
    • Panchenko AR. Finding weak similarities between proteins by sequence profile comparison. Nucleic Acids Res 2003; 31: 683-689.
    • (2003) Nucleic Acids Res , vol.31 , pp. 683-689
    • Panchenko, A.R.1
  • 16
    • 0043130635 scopus 로고    scopus 로고
    • Profile-profile alignment: a powerful tool for protein structure prediction
    • von Ohsen N, Sommer I, Zimmer R. Profile-profile alignment: a powerful tool for protein structure prediction. Pac Symp Biocomput 2003: 252-263.
    • (2003) Pac Symp Biocomput , pp. 252-263
    • von Ohsen, N.1    Sommer, I.2    Zimmer, R.3
  • 17
    • 0141634362 scopus 로고    scopus 로고
    • Profile-profile comparisons by COMPASS predict intricate homologies between protein families
    • Sadreyev RI, Baker D, Grishin NV. Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein Sci 2003; 12: 2262-2272.
    • (2003) Protein Sci , vol.12 , pp. 2262-2272
    • Sadreyev, R.I.1    Baker, D.2    Grishin, N.V.3
  • 18
    • 0345827718 scopus 로고    scopus 로고
    • Using evolutionary information for the query and target improves fold recognition
    • Wallner B, Fang H, Ohlson T, Frey-Skott J, Elofsson A. Using evolutionary information for the query and target improves fold recognition. Proteins 2004; 54: 342-350.
    • (2004) Proteins , vol.54 , pp. 342-350
    • Wallner, B.1    Fang, H.2    Ohlson, T.3    Frey-Skott, J.4    Elofsson, A.5
  • 19
    • 58149187899 scopus 로고    scopus 로고
    • The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies
    • Database issue
    • Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton J, Orengo CA. The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res 2009; 37 (Database issue): D310-D314.
    • (2009) Nucleic Acids Res , vol.37
    • Cuff, A.L.1    Sillitoe, I.2    Lewis, T.3    Redfern, O.C.4    Garratt, R.5    Thornton, J.6    Orengo, C.A.7
  • 23
    • 3042581007 scopus 로고    scopus 로고
    • Flexible structure alignment by chaining aligned fragment pairs allowing twists
    • Ye Y, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics 2003; 19 ( Suppl 2): ii246-ii255.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Ye, Y.1    Godzik, A.2
  • 24
    • 37549012936 scopus 로고    scopus 로고
    • Contributions to the NIH-NIGMS protein structure initiative from the PSI production centers
    • Burley SK, Joachimiak A, Montelione GT, Wilson IA. Contributions to the NIH-NIGMS protein structure initiative from the PSI production centers. Structure 2008; 16: 5-11.
    • (2008) Structure , vol.16 , pp. 5-11
    • Burley, S.K.1    Joachimiak, A.2    Montelione, G.T.3    Wilson, I.A.4
  • 27
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • 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.
    • (2006) Bioinformatics , vol.22 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 28
    • 3242887315 scopus 로고    scopus 로고
    • FATCAT: a web server for flexible structure comparison and structure similarity searching
    • Web Server issue
    • Ye Y, Godzik A. FATCAT: a web server for flexible structure comparison and structure similarity searching. Nucleic Acids Res 2004; 32 (Web Server issue): W582-W585.
    • (2004) Nucleic Acids Res , vol.32
    • Ye, Y.1    Godzik, A.2
  • 29
    • 0033846832 scopus 로고    scopus 로고
    • Improving the quality of twilight-zone alignments
    • Jaroszewski L, Rychlewski L, Godzik A. Improving the quality of twilight-zone alignments. Protein Sci 2000; 9: 1487-1496.
    • (2000) Protein Sci , vol.9 , pp. 1487-1496
    • Jaroszewski, L.1    Rychlewski, L.2    Godzik, A.3
  • 30
    • 34147167680 scopus 로고    scopus 로고
    • On the relationship between sequence and structure similarities in proteomics
    • Krissinel E. On the relationship between sequence and structure similarities in proteomics. Bioinformatics 2007; 23: 717-723.
    • (2007) Bioinformatics , vol.23 , pp. 717-723
    • Krissinel, E.1
  • 31
    • 1542358787 scopus 로고    scopus 로고
    • Prediction and functional analysis of native disorder in proteins from the three kingdoms of life
    • Ward JJ, Sodhi JS, McGuffin LJ, Buxton BF, Jones DT. Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J Mol Biol 2004; 337: 635-645.
    • (2004) J Mol Biol , vol.337 , pp. 635-645
    • Ward, J.J.1    Sodhi, J.S.2    McGuffin, L.J.3    Buxton, B.F.4    Jones, D.T.5
  • 34
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with rosetta
    • Das R, Baker D. Macromolecular modeling with rosetta. Annu Rev Biochem 2008; 77: 363-382.
    • (2008) Annu Rev Biochem , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.