메뉴 건너뛰기




Volumn 42, Issue D1, 2014, Pages

Pfam: The protein families database

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEOME; INTRINSICALLY DISORDERED PROTEIN; PROTEIN;

EID: 84891782659     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkt1223     Document Type: Review
Times cited : (4858)

References (40)
  • 1
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology. Applications to protein modeling
    • Krogh, A., Brown, M., Mian, I.S., Sjolander, K. and Haussler, D. (1994) Hidden Markov models in computational biology. Applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, I.S.3    Sjolander, K.4    Haussler, D.5
  • 2
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy, S.R. (1998) Profile hidden Markov models. Bioinformatics, 14, 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 3
    • 84860833500 scopus 로고    scopus 로고
    • Reorganizing the protein space at the Universal Protein Resource (UniProt)
    • UniProt Consortium.
    • UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res., 40, D71-D75.
    • (2012) Nucleic Acids Res. , vol.40
  • 4
    • 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
  • 5
    • 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
    • Eddy, S.R.1
  • 12
    • 65449188232 scopus 로고    scopus 로고
    • Jalview Version 2-A multiple sequence alignment editor and analysis workbench
    • Waterhouse, A.M., Procter, J.B., Martin, D.M.A., Clamp, M. and Barton, G.J. (2009) Jalview Version 2-A multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
    • (2009) Bioinformatics , vol.25 , pp. 1189-1191
    • Waterhouse, A.M.1    Procter, J.B.2    Martin, D.M.A.3    Clamp, M.4    Barton, G.J.5
  • 13
    • 79955684513 scopus 로고    scopus 로고
    • Representative proteomes: A stable, scalable and unbiased proteome set for sequence analysis and functional annotation
    • Chen, C., Natale, D.A., Finn, R.D., Huang, H., Zhang, J., Wu, C.H. and Mazumder, R. (2011) Representative proteomes: a stable, scalable and unbiased proteome set for sequence analysis and functional annotation. PLoS One, 6, e18910.
    • (2011) PLoS One , vol.6
    • Chen, C.1    Natale, D.A.2    Finn, R.D.3    Huang, H.4    Zhang, J.5    Wu, C.H.6    Mazumder, R.7
  • 14
    • 77949718257 scopus 로고    scopus 로고
    • FastTree 2- approximately maximum-likelihood trees for large alignments
    • Price, M.N., Dehal, P.S. and Arkin, A.P. (2010) FastTree 2- approximately maximum-likelihood trees for large alignments. PLoS One, 5, e9490.
    • (2010) PLoS One , vol.5
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 18
  • 19
    • 84876532610 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information
    • NCBI Resource Coordinators.
    • NCBI Resource Coordinators. (2013) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 41, D8-D20.
    • (2013) Nucleic Acids Res. , vol.41
  • 21
    • 2942576060 scopus 로고    scopus 로고
    • Enhanced protein domain discovery using taxonomy
    • Coin, L., Bateman, A. and Durbin, R. (2004) Enhanced protein domain discovery using taxonomy. BMC Bioinformatics, 5, 56.
    • (2004) BMC Bioinformatics , vol.5 , pp. 56
    • Coin, L.1    Bateman, A.2    Durbin, R.3
  • 22
    • 34248576303 scopus 로고    scopus 로고
    • Functional evaluation of domain-domain interactions and human protein interaction networks
    • Schlicker, A., Huthmacher, C., Ramirez, F., Lengauer, T. and Albrecht, M. (2007) Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics, 23, 859-865.
    • (2007) Bioinformatics , vol.23 , pp. 859-865
    • Schlicker, A.1    Huthmacher, C.2    Ramirez, F.3    Lengauer, T.4    Albrecht, M.5
  • 23
    • 43149094164 scopus 로고    scopus 로고
    • Pfam 10 years on: 10, 000 families and still growing
    • Sammut, S.J., Finn, R.D. and Bateman, A. (2008) Pfam 10 years on: 10, 000 families and still growing. Brief. Bioinformatics, 9, 210-219.
    • (2008) Brief. Bioinformatics , vol.9 , pp. 210-219
    • Sammut, S.J.1    Finn, R.D.2    Bateman, A.3
  • 24
    • 0033982651 scopus 로고    scopus 로고
    • Role of linkers in communication between protein modules
    • Gokhale, R.S. and Khosla, C. (2000) Role of linkers in communication between protein modules. Curr. Opin. Chem. Biol., 4, 22-27.
    • (2000) Curr. Opin. Chem. Biol. , vol.4 , pp. 22-27
    • Gokhale, R.S.1    Khosla, C.2
  • 25
    • 0036878154 scopus 로고    scopus 로고
    • An analysis of protein domain linkers: Their classification and role in protein folding
    • George, R.A. and Heringa, J. (2002) An analysis of protein domain linkers: their classification and role in protein folding. Protein Eng., 15, 871-879.
    • (2002) Protein Eng. , vol.15 , pp. 871-879
    • George, R.A.1    Heringa, J.2
  • 26
    • 33144464467 scopus 로고    scopus 로고
    • Control of protein functional dynamics by peptide linkers
    • Wriggers, W., Chakravarty, S. and Jennings, P.A. (2005) Control of protein functional dynamics by peptide linkers. Biopolymers., 80, 736-746.
    • (2005) Biopolymers. , vol.80 , pp. 736-746
    • Wriggers, W.1    Chakravarty, S.2    Jennings, P.A.3
  • 27
    • 84874033858 scopus 로고    scopus 로고
    • Linkers in the structural biology of protein-protein interactions
    • Reddy Chichili, V.P., Kumar, V. and Sivaraman, J. (2013) Linkers in the structural biology of protein-protein interactions. Protein Sci., 22, 153-167.
    • (2013) Protein Sci. , vol.22 , pp. 153-167
    • Reddy Chichili, V.P.1    Kumar, V.2    Sivaraman, J.3
  • 28
    • 2142657817 scopus 로고    scopus 로고
    • A combined transmembrane topology and signal peptide prediction method
    • Kall, L., Krogh, A. and Sonnhammer, E.L.L. (2004) A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol., 338, 1027-1036.
    • (2004) J. Mol. Biol. , vol.338 , pp. 1027-1036
    • Kall, L.1    Krogh, A.2    Sonnhammer, E.L.L.3
  • 29
    • 0028501914 scopus 로고
    • Non-globular domains in protein sequences: Automated segmentation using complexity measures
    • Wootton, J.C. (1994) Non-globular domains in protein sequences: automated segmentation using complexity measures. Comput. Chem., 18, 269-285.
    • (1994) Comput. Chem. , vol.18 , pp. 269-285
    • Wootton, J.C.1
  • 30
    • 73449123761 scopus 로고    scopus 로고
    • Unfoldomics of human genetic diseases: Illustrative examples of ordered and intrinsically disordered members of the human diseasome
    • Midic, U., Oldfield, C.J., Dunker, A.K., Obradovic, Z. and Uversky, V.N. (2009) Unfoldomics of human genetic diseases: illustrative examples of ordered and intrinsically disordered members of the human diseasome. Protein Pept. Lett., 16, 1533-1547.
    • (2009) Protein Pept. Lett. , vol.16 , pp. 1533-1547
    • Midic, U.1    Oldfield, C.J.2    Dunker, A.K.3    Obradovic, Z.4    Uversky, V.N.5
  • 32
    • 82655181911 scopus 로고    scopus 로고
    • Intrinsic disorder in cell signaling and gene transcription
    • Tantos, A., Han, K.H. and Tompa, P. (2012) Intrinsic disorder in cell signaling and gene transcription. Mol. Cell. Endocrinol., 348, 457-465.
    • (2012) Mol. Cell. Endocrinol. , vol.348 , pp. 457-465
    • Tantos, A.1    Han, K.H.2    Tompa, P.3
  • 34
    • 14844342815 scopus 로고    scopus 로고
    • The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins
    • Dosztanyi, Z., Csizmok, V., Tompa, P. and Simon, I. (2005) The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. J. Mol. Biol., 347, 827-839.
    • (2005) J. Mol. Biol. , vol.347 , pp. 827-839
    • Dosztanyi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 35
    • 24044538903 scopus 로고    scopus 로고
    • IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content
    • Dosztanyi, Z., Csizmok, V., Tompa, P. and Simon, I. (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434.
    • (2005) Bioinformatics , vol.21 , pp. 3433-3434
    • Dosztanyi, Z.1    Csizmok, V.2    Tompa, P.3    Simon, I.4
  • 36
    • 84868027251 scopus 로고    scopus 로고
    • Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB
    • Xu, Q. and Dunbrack, R.L. (2012) Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. Bioinformatics, 28, 2763-2772.
    • (2012) Bioinformatics , vol.28 , pp. 2763-2772
    • Xu, Q.1    Dunbrack, R.L.2
  • 37
    • 2142639533 scopus 로고    scopus 로고
    • Determination of structural principles underlying three different modes of lymphocytic choriomeningitis virus escape from CTL recognition
    • Velloso, L.M., Michaelsson, J., Ljunggren, H.G., Schneider, G. and Achour, A. (2004) Determination of structural principles underlying three different modes of lymphocytic choriomeningitis virus escape from CTL recognition. J. Immunol., 172, 5504-5511.
    • (2004) J. Immunol. , vol.172 , pp. 5504-5511
    • Velloso, L.M.1    Michaelsson, J.2    Ljunggren, H.G.3    Schneider, G.4    Achour, A.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.