메뉴 건너뛰기




Volumn 43, Issue W1, 2015, Pages W148-W153

CATH FunFHMMer web server: Protein functional annotations using functional family assignments

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; AMINO ACID SEQUENCE; ARTICLE; CATH FUNFHMMER WEB SERVER; GENE ONTOLOGY; HIDDEN MARKOV MODEL; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN DOMAIN; SEQUENCE ALIGNMENT; VALIDATION PROCESS; WEB BROWSER; CLASSIFICATION; COMPUTER PROGRAM; GENETICS; INTERNET; MOLECULAR GENETICS; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE;

EID: 84979865064     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv488     Document Type: Article
Times cited : (47)

References (29)
  • 2
    • 0034308142 scopus 로고    scopus 로고
    • Practical limits of function prediction
    • Devos, D. and Valencia, A. (2000) Practical limits of function prediction. Proteins, 41, 98-107.
    • (2000) Proteins , vol.41 , pp. 98-107
    • Devos, D.1    Valencia, A.2
  • 3
    • 55449125498 scopus 로고    scopus 로고
    • The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function
    • Punta, M. and Ofran, Y. (2008) The rough guide to in silico function prediction, or how to use sequence and structure information to predict protein function. PLoS Comput. Biol., 4, e1000160.
    • (2008) PLoS Comput. Biol. , vol.4 , pp. e1000160
    • Punta, M.1    Ofran, Y.2
  • 4
    • 0037075039 scopus 로고    scopus 로고
    • Orthology: Secret life of genes
    • Theißen, G. (2002) Orthology: secret life of genes. Nature, 415, 741.
    • (2002) Nature , vol.415 , pp. 741
    • Theißen, G.1
  • 5
  • 6
    • 0009130599 scopus 로고    scopus 로고
    • A structural explanation for the twilight zone of protein sequence homology
    • Chung, S.Y. and Subbiah, S. (1996) A structural explanation for the twilight zone of protein sequence homology. Structure, 4, 1123-1127.
    • (1996) Structure , vol.4 , pp. 1123-1127
    • Chung, S.Y.1    Subbiah, S.2
  • 7
    • 33846059668 scopus 로고    scopus 로고
    • The generation of new protein functions by the combination of domains
    • Bashton, M. and Chothia, C. (2007) The generation of new protein functions by the combination of domains. Structure, 15, 85-99.
    • (2007) Structure , vol.15 , pp. 85-99
    • Bashton, M.1    Chothia, C.2
  • 8
    • 0035424599 scopus 로고    scopus 로고
    • Intrinsic errors in genome annotation
    • Devos, D. and Valencia, A. (2001) Intrinsic errors in genome annotation. Trends Genet., 17, 429-431.
    • (2001) Trends Genet. , vol.17 , pp. 429-431
    • Devos, D.1    Valencia, A.2
  • 9
    • 36448988254 scopus 로고    scopus 로고
    • Predicting protein function from sequence and structure
    • Lee, D., Redfern, O.C. and Orengo, C.A. (2007) Predicting protein function from sequence and structure. Nat. Rev. Mol. Cell Biol., 8, 995-1005.
    • (2007) Nat. Rev. Mol. Cell Biol. , vol.8 , pp. 995-1005
    • Lee, D.1    Redfern, O.C.2    Orengo, C.A.3
  • 10
    • 66549096455 scopus 로고    scopus 로고
    • Exploiting structural classifications for function prediction: Towards a domain grammar for protein function
    • Dessailly, B.H., Redfern, O.C., Cuff, A. and Orengo, C.A. (2009) Exploiting structural classifications for function prediction: towards a domain grammar for protein function. Curr. Opin. Struct. Biol., 19, 349-356.
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 349-356
    • Dessailly, B.H.1    Redfern, O.C.2    Cuff, A.3    Orengo, C.A.4
  • 11
    • 84876298530 scopus 로고    scopus 로고
    • Protein function prediction using domain families
    • Rentzsch, R. and Orengo, C.A. (2013) Protein function prediction using domain families. BMC Bioinformatics, 14, S5.
    • (2013) BMC Bioinformatics , vol.14 , pp. S5
    • Rentzsch, R.1    Orengo, C.A.2
  • 13
    • 85016017902 scopus 로고    scopus 로고
    • Automated sequence-based approaches for identifying domain families
    • Orengo, CA and Bateman, A (eds). John Wiley & Sons, Inc., Hoboken, NJ
    • Holm, L. and Heger, A. (2013) Automated sequence-based approaches for identifying domain families. In: Orengo, CA and Bateman, A (eds). Protein Families: Relating Protein Sequence, Structure, and Function. John Wiley & Sons, Inc., Hoboken, NJ, pp. 1-24.
    • (2013) Protein Families: Relating Protein Sequence, Structure, and Function , pp. 1-24
    • Holm, L.1    Heger, A.2
  • 16
    • 77951946371 scopus 로고    scopus 로고
    • A fast and automated solution for accurately resolving protein domain architectures
    • Yeats, C., Redfern, O.C. and Orengo, C.A. (2010) A fast and automated solution for accurately resolving protein domain architectures. Bioinformatics, 26, 745-751.
    • (2010) Bioinformatics , vol.26 , pp. 745-751
    • Yeats, C.1    Redfern, O.C.2    Orengo, C.A.3
  • 17
    • 79960610118 scopus 로고    scopus 로고
    • Revigo summarizes and visualizes long lists of gene ontology terms
    • Supek, F., Bošnjak, M., Škunca, N. and Šmuc, T. (2011) Revigo summarizes and visualizes long lists of gene ontology terms. PloS One, 6, e21800.
    • (2011) PloS One , vol.6 , pp. e21800
    • Supek, F.1    Bošnjak, M.2    Škunca, N.3    Šmuc, T.4
  • 19
    • 0035815113 scopus 로고    scopus 로고
    • Evolution of function in protein superfamilies, from a structural perspective
    • Todd, A.E, Orengo, C.A. and Thornton, J.M. (2001) Evolution of function in protein superfamilies, from a structural perspective. J. Mol. Biol., 307, 1113-1143.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1113-1143
    • Todd, A.E.1    Orengo, C.A.2    Thornton, J.M.3
  • 20
    • 77950362058 scopus 로고    scopus 로고
    • Gemma: Functional subfamily classification within superfamilies of predicted protein structural domains
    • Lee, D., Rentzsch, R. and Orengo, C.A. (2010) Gemma: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Res., 38, 720-737.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 720-737
    • Lee, D.1    Rentzsch, R.2    Orengo, C.A.3
  • 21
    • 0037100671 scopus 로고    scopus 로고
    • Mafft: A novel method for rapid multiple sequence alignment based on fast fourier transform
    • Katoh, K., Misawa, K., Kuma, K. and Miyata, T. (2002) Mafft: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res., 30, 3059-3066.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3059-3066
    • Katoh, K.1    Misawa, K.2    Kuma, K.3    Miyata, T.4
  • 22
    • 77952988108 scopus 로고    scopus 로고
    • A new generation of homology search tools based on probabilistic inference
    • Eddy, S.R. (2009) A new generation of homology search tools based on probabilistic inference. Genome Inform., 23, 205-211.
    • (2009) Genome Inform. , vol.23 , pp. 205-211
    • Eddy, S.R.1
  • 23
    • 84863693531 scopus 로고    scopus 로고
    • Quality of computationally inferred gene ontology annotations
    • Škunca, N., Altenhoff, A. and Dessimoz, C. (2012) Quality of computationally inferred gene ontology annotations. PLoS Comput. Biol., 8, e1002533.
    • (2012) PLoS Comput. Biol. , vol.8 , pp. e1002533
    • Škunca, N.1    Altenhoff, A.2    Dessimoz, C.3
  • 24
    • 80055082271 scopus 로고    scopus 로고
    • Accelerated profile HMM searches
    • Eddy, S.R. (2011) Accelerated Profile HMM Searches. PLoS comput. Biol., 7, e1002195.
    • (2011) PLoS Comput. Biol. , vol.7 , pp. e1002195
    • Eddy, S.R.1
  • 28
    • 24044478768 scopus 로고    scopus 로고
    • MagicMatchcross-referencing sequence identifiers across databases
    • Smith, M., Kunin, V., Goldovsky, L., Enright, A.J. and Ouzounis, C.A. (2005) MagicMatchcross-referencing sequence identifiers across databases. Bioinformatics, 2116, 3429-3430.
    • (2005) Bioinformatics , vol.2116 , pp. 3429-3430
    • Smith, M.1    Kunin, V.2    Goldovsky, L.3    Enright, A.J.4    Ouzounis, C.A.5
  • 29
    • 0036681416 scopus 로고    scopus 로고
    • Scoring residue conservation
    • Valdar, W.S.J. (2002) Scoring residue conservation. Proteins, 48, 227-241.
    • (2002) Proteins , vol.48 , pp. 227-241
    • Valdar, W.S.J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.