-
1
-
-
0037250523
-
ProtoNet: Hierarchical classification of the protein space
-
DOI 10.1093/nar/gkg096
-
Sasson,O., Vaaknin,A., Fleischer,H., Portugaly,E., Bilu,Y., Linial,N. and Linial,M. (2003) ProtoNet: hierarchical classification of the protein space. Nucleic Acids Res., 31, 348-352. (Pubitemid 36150401)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 348-352
-
-
Sasson, O.1
Vaaknin, A.2
Fleischer, H.3
Portugaly, E.4
Bilu, Y.5
Linial, N.6
Linial, M.7
-
2
-
-
75849153303
-
The Universal Protein Resource (UniProt) in 2010
-
The UniProt Consortium
-
The UniProt Consortium. (2011) The Universal Protein Resource (UniProt) in 2010. Nucleic Acids Res., 38, D142-D148.
-
(2011)
Nucleic Acids Res.
, vol.38
-
-
-
3
-
-
60749125063
-
Protein function annotation by homology-based inference
-
Loewenstein,Y., Raimondo,D., Redfern,O.C., Watson,J., Frishman,D., Linial,M., Orengo,C., Thornton,J. and Tramontano,A. (2009) Protein function annotation by homology-based inference. Genome Biol., 10, 207.
-
(2009)
Genome Biol.
, vol.10
, pp. 207
-
-
Loewenstein, Y.1
Raimondo, D.2
Redfern, O.C.3
Watson, J.4
Frishman, D.5
Linial, M.6
Orengo, C.7
Thornton, J.8
Tramontano, A.9
-
4
-
-
0344417851
-
A novel method for automatic functional annotation of proteins
-
DOI 10.1093/bioinformatics/15.3.228
-
Fleischmann,W., Moller,S., Gateau,A. and Apweiler,R. (1999) A novel method for automatic functional annotation of proteins. Bioinformatics, 15, 228-233. (Pubitemid 29197000)
-
(1999)
Bioinformatics
, vol.15
, Issue.3
, pp. 228-233
-
-
Fleischmann, W.1
Moller, S.2
Gateau, A.3
Apweiler, R.4
-
5
-
-
33748776559
-
Automated protein function prediction-the genomic challenge
-
Friedberg,I. (2006) Automated protein function prediction-the genomic challenge. Brief Bioinform., 7, 225-242.
-
(2006)
Brief Bioinform.
, vol.7
, pp. 225-242
-
-
Friedberg, I.1
-
6
-
-
34548392746
-
Automated protein subfamily identification and classification
-
Brown,D.P., Krishnamurthy,N. and Sjolander,K. (2007) Automated protein subfamily identification and classification. PLoS Comput. Biol., 3, e160.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Brown, D.P.1
Krishnamurthy, N.2
Sjolander, K.3
-
7
-
-
33947278347
-
Towards Fully Automated Structure-based Function Prediction in Structural Genomics: A Case Study
-
DOI 10.1016/j.jmb.2007.01.063, PII S0022283607001167
-
Watson,J.D., Sanderson,S., Ezersky,A., Savchenko,A., Edwards,A., Orengo,C., Joachimiak,A., Laskowski,R.A. and Thornton,J.M. (2007) Towards fully automated structure-based function prediction in structural genomics: a case study. J. Mol. Biol., 367, 1511-1522. (Pubitemid 46420706)
-
(2007)
Journal of Molecular Biology
, vol.367
, Issue.5
, pp. 1511-1522
-
-
Watson, J.D.1
Sanderson, S.2
Ezersky, A.3
Savchenko, A.4
Edwards, A.5
Orengo, C.6
Joachimiak, A.7
Laskowski, R.A.8
Thornton, J.M.9
-
9
-
-
75549090603
-
The Pfam protein families database
-
Finn,R.D., Mistry,J., Tate,J., Coggill,P., Heger,A., Pollington,J.E., Gavin,O.L., Gunasekaran,P., Ceric,G., Forslund,K. et al. (2010) The Pfam protein families database. Nucleic Acids Res., 38, D211-D222.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Finn, R.D.1
Mistry, J.2
Tate, J.3
Coggill, P.4
Heger, A.5
Pollington, J.E.6
Gavin, O.L.7
Gunasekaran, P.8
Ceric, G.9
Forslund, K.10
-
10
-
-
58149194624
-
SMART 6: Recent updates and new developments
-
Letunic,I., Doerks,T. and Bork,P. (2009) SMART 6: recent updates and new developments. Nucleic Acids Res., 37, D229-D232.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Letunic, I.1
Doerks, T.2
Bork, P.3
-
11
-
-
33846079070
-
EVEREST: A collection of evolutionary conserved protein domains
-
DOI 10.1093/nar/gkl850
-
Portugaly,E., Linial,N. and Linial,M. (2007) EVEREST: a collection of evolutionary conserved protein domains. Nucleic Acids Res., 35, D241-D246. (Pubitemid 46056207)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Portugaly, E.1
Linial, N.2
Linial, M.3
-
12
-
-
75549084894
-
PANTHER version 7: Improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium
-
Mi,H., Dong,Q., Muruganujan,A., Gaudet,P., Lewis,S. and Thomas,P.D. (2010) PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. Nucleic Acids Res., 38, D204-D210.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Mi, H.1
Dong, Q.2
Muruganujan, A.3
Gaudet, P.4
Lewis, S.5
Thomas, P.D.6
-
13
-
-
79960029950
-
The Gene3D Web Services: A platform for identifying, annotating and comparing structural domains in protein sequences
-
Yeats,C., Lees,J., Carter,P., Sillitoe,I. and Orengo,C. (2011) The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. Nucleic Acids Res., 39, W546-W550.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Yeats, C.1
Lees, J.2
Carter, P.3
Sillitoe, I.4
Orengo, C.5
-
14
-
-
75549087533
-
PROSITE, a protein domain database for functional characterization and annotation
-
Sigrist,C.J., Cerutti,L., de Castro,E., Langendijk-Genevaux,P.S., Bulliard,V., Bairoch,A. and Hulo,N. (2010) PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res., 38, D161-D166.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Sigrist, C.J.1
Cerutti, L.2
De Castro, E.3
Langendijk-Genevaux, P.S.4
Bulliard, V.5
Bairoch, A.6
Hulo, N.7
-
15
-
-
0037248869
-
PRINTS and its automatic supplement, prePRINTS
-
DOI 10.1093/nar/gkg030
-
Attwood,T.K., Bradley,P., Flower,D.R., Gaulton,A., Maudling,N., Mitchell,A.L., Moulton,G., Nordle,A., Paine,K., Taylor,P. et al. (2003) PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res., 31, 400-402. (Pubitemid 36150412)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 400-402
-
-
Attwood, T.K.1
Bradley, P.2
Flower, D.R.3
Gaulton, A.4
Maudling, N.5
Mitchell, A.L.6
Moulton, G.7
Nordle, A.8
Paine, K.9
Taylor, P.10
Uddin, A.11
Zygouri, C.12
-
16
-
-
13444305296
-
The ProDom database of protein domain families: More emphasis on 3D
-
DOI 10.1093/nar/gki034
-
Bru,C., Courcelle,E., Carrere,S., Beausse,Y., Dalmar,S. and Kahn,D. (2005) The ProDom database of protein domain families: more emphasis on 3D. Nucleic Acids Res., 33, D212-D215. (Pubitemid 40207862)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Bru, C.1
Courcelle, E.2
Carrere, S.3
Beausse, Y.4
Dalmar, S.5
Kahn, D.6
-
17
-
-
0033977579
-
Increased coverage of protein families with the Blocks Database servers
-
Henikoff,J.G., Greene,E.A., Pietrokovski,S. and Henikoff,S. (2000) Increased coverage of protein families with the blocks database servers. Nucleic Acids Res., 28, 228-230. (Pubitemid 30047766)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 228-230
-
-
Henikoff, J.G.1
Greene, E.A.2
Pietrokovski, S.3
Henikoff, S.4
-
18
-
-
9144231826
-
PIRSF: Family classification system at the Protein Information Resource
-
Wu,C.H., Nikolskaya,A., Huang,H., Yeh,L.S., Natale,D.A., Vinayaka,C.R., Hu,Z.Z., Mazumder,R., Kumar,S., Kourtesis,P. et al. (2004) PIRSF: family classification system at the Protein Information Resource. Nucleic Acids Res., 32, D112-D114. (Pubitemid 38081616)
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.DATABASE ISS.
-
-
Wu, C.H.1
Nikolskaya, A.2
Huang, H.3
Yeh, L.-S.4
Natale, D.A.5
Vinayaka, C.R.6
Hu, Z.-Z.7
Mazumder, R.8
Kumar, S.9
Kourtesis, P.10
Ledley, R.S.11
Suzek, B.E.12
Arminski, L.13
Chen, Y.14
Zhang, J.15
Cardenas, J.L.16
Chung, S.17
Castro-Alvear, J.18
Dinkov, G.19
Barker, W.C.20
more..
-
19
-
-
78651285748
-
CDD: A Conserved Domain Database for the functional annotation of proteins
-
Marchler-Bauer,A., Lu,S., Anderson,J.B., Chitsaz,F., Derbyshire,M.K., DeWeese-Scott,C., Fong,J.H., Geer,L.Y., Geer,R.C., Gonzales,N.R. et al. (2010) CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic Acids Res., 39, D225-D229.
-
(2010)
Nucleic Acids Res.
, vol.39
-
-
Marchler-Bauer, A.1
Lu, S.2
Anderson, J.B.3
Chitsaz, F.4
Derbyshire, M.K.5
DeWeese-Scott, C.6
Fong, J.H.7
Geer, L.Y.8
Geer, R.C.9
Gonzales, N.R.10
-
20
-
-
58149203231
-
InterPro: The integrative protein signature database
-
Hunter,S., Apweiler,R., Attwood,T.K., Bairoch,A., Bateman,A., Binns,D., Bork,P., Das,U., Daugherty,L., Duquenne,L. et al. (2009) InterPro: the integrative protein signature database. Nucleic Acids Res., 37, D211-D215.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Hunter, S.1
Apweiler, R.2
Attwood, T.K.3
Bairoch, A.4
Bateman, A.5
Binns, D.6
Bork, P.7
Das, U.8
Daugherty, L.9
Duquenne, L.10
-
21
-
-
38549153238
-
Data growth and its impact on the SCOP database: New developments
-
DOI 10.1093/nar/gkm993
-
Andreeva,A., Howorth,D., Chandonia,J.M., Brenner,S.E., Hubbard,T.J., Chothia,C. and Murzin,A.G. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res., 36, D419-D425. (Pubitemid 351149760)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.SUPPL. 1
-
-
Andreeva, A.1
Howorth, D.2
Chandonia, J.-M.3
Brenner, S.E.4
Hubbard, T.J.P.5
Chothia, C.6
Murzin, A.G.7
-
22
-
-
58149187899
-
The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies
-
Cuff,A.L., Sillitoe,I., Lewis,T., Redfern,O.C., Garratt,R., Thornton,J. and Orengo,C.A. (2009) The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies. Nucleic Acids Res., 37, 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
-
-
13444272079
-
The CATH domain structure database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis
-
DOI 10.1093/nar/gki024
-
Pearl,F., Todd,A., Sillitoe,I., Dibley,M., Redfern,O., Lewis,T., Bennett,C., Marsden,R., Grant,A., Lee,D. et al. (2005) The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Res., 33, D247-D251. (Pubitemid 40207871)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Pearl, F.1
Todd, A.2
Sillitoe, I.3
Dibley, M.4
Redfern, O.5
Lewis, T.6
Bennett, C.7
Marsden, R.8
Grant, A.9
Lee, D.10
Akpor, A.11
Maibaum, M.12
Harrison, A.13
Dallman, T.14
Reeves, G.15
Diboun, I.16
Addou, S.17
Lise, S.18
Johnston, C.19
Sillero, A.20
Thornton, J.21
Orengo, C.22
more..
-
24
-
-
58149187893
-
The GOA database in 2009-an integrated Gene Ontology Annotation resource
-
Barrell,D., Dimmer,E., Huntley,R.P., Binns,D., O'Donovan,C. and Apweiler,R. (2009) The GOA database in 2009-an integrated Gene Ontology Annotation resource. Nucleic Acids Res., 37, D396-D403.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Barrell, D.1
Dimmer, E.2
Huntley, R.P.3
Binns, D.4
O'Donovan, C.5
Apweiler, R.6
-
25
-
-
34347388470
-
UniRef: Comprehensive and non-redundant UniProt reference clusters
-
DOI 10.1093/bioinformatics/btm098
-
Suzek,B.E., Huang,H., McGarvey,P., Mazumder,R. and Wu,C.H. (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics, 23, 1282-1288. (Pubitemid 47050545)
-
(2007)
Bioinformatics
, vol.23
, Issue.10
, pp. 1282-1288
-
-
Suzek, B.E.1
Huang, H.2
McGarvey, P.3
Mazumder, R.4
Wu, C.H.5
-
26
-
-
13244285287
-
ProtoNet 4.0: A hierarchical classification of one million protein sequences
-
DOI 10.1093/nar/gki007
-
Kaplan,N., Sasson,O., Inbar,U., Friedlich,M., Fromer,M., Fleischer,H., Portugaly,E., Linial,N. and Linial,M. (2005) ProtoNet 4.0: a hierarchical classification of one million protein sequences. Nucleic Acids Res., 33, D216-D218. (Pubitemid 40207863)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Kaplan, N.1
Sasson, O.2
Inbar, U.3
Friedlinch, M.4
Fromer, M.5
Fleischer, H.6
Portugaly, E.7
Linial, N.8
Linial, M.9
-
27
-
-
33744482316
-
Functional annotation prediction: All for one and one for all
-
DOI 10.1110/ps.062185706
-
Sasson,O., Kaplan,N. and Linial,M. (2006) Functional annotation prediction: all for one and one for all. Protein Sci., 15, 1557-1562. (Pubitemid 43800031)
-
(2006)
Protein Science
, vol.15
, Issue.6
, pp. 1557-1562
-
-
Sasson, O.1
Kaplan, N.2
Linial, M.3
-
28
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
DOI 10.1093/nar/25.17.3389
-
Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402. (Pubitemid 27359211)
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.17
, pp. 3389-3402
-
-
Altschul, S.F.1
Madden, T.L.2
Schaffer, A.A.3
Zhang, J.4
Zhang, Z.5
Miller, W.6
Lipman, D.J.7
-
29
-
-
46249133773
-
Efficient algorithms for accurate hierarchical clustering of huge datasets: Tackling the entire protein space
-
DOI 10.1093/bioinformatics/btn174
-
Loewenstein,Y., Portugaly,E., Fromer,M. and Linial,M. (2008) Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space. Bioinformatics, 24, i41-i49. (Pubitemid 351911656)
-
(2008)
Bioinformatics
, vol.24
, Issue.13
-
-
Loewenstein, Y.1
Portugaly, E.2
Fromer, M.3
Linial, M.4
-
30
-
-
24644474560
-
The predictive power of the CluSTr database
-
DOI 10.1093/bioinformatics/bti542
-
Petryszak,R., Kretschmann,E., Wieser,D. and Apweiler,R. (2005) The predictive power of the CluSTr database. Bioinformatics, 21, 3604-3609. (Pubitemid 41264094)
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3604-3609
-
-
Petryszak, R.1
Kretschmann, E.2
Wieser, D.3
Apweiler, R.4
-
31
-
-
0033963089
-
The ENZYME database in 2000
-
Bairoch,A. (2000) The ENZYME database in 2000. Nucleic Acids Res., 28, 304-305.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 304-305
-
-
Bairoch, A.1
-
32
-
-
77954267418
-
PANDORA: Analysis of protein and peptide sets through the hierarchical integration of annotations
-
Rappoport,N., Fromer,M., Schweiger,R. and Linial,M. (2010) PANDORA: analysis of protein and peptide sets through the hierarchical integration of annotations. Nucleic Acids Res., 38, W84-W89.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Rappoport, N.1
Fromer, M.2
Schweiger, R.3
Linial, M.4
-
33
-
-
33947235074
-
The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families
-
Yooseph,S., Sutton,G., Rusch,D.B., Halpern,A.L., Williamson,S.J., Remington,K., Eisen,J.A., Heidelberg,K.B., Manning,G., Li,W. et al. (2007) The Sorcerer II Global Ocean Sampling expedition: expanding the universe of protein families. PLoS Biol., 5, e16.
-
(2007)
PLoS Biol.
, vol.5
-
-
Yooseph, S.1
Sutton, G.2
Rusch, D.B.3
Halpern, A.L.4
Williamson, S.J.5
Remington, K.6
Eisen, J.A.7
Heidelberg, K.B.8
Manning, G.9
Li, W.10
|