-
2
-
-
16244423379
-
Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions
-
10.1016/j.jmb.2005.02.007, 15808866
-
Ekman D, Bjorklund AK, Frey-Skott J, Elofsson A. Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. Journal of molecular biology 2005, 348(1):231-243. 10.1016/j.jmb.2005.02.007, 15808866.
-
(2005)
Journal of molecular biology
, vol.348
, Issue.1
, pp. 231-243
-
-
Ekman, D.1
Bjorklund, A.K.2
Frey-Skott, J.3
Elofsson, A.4
-
3
-
-
0037841804
-
Evolution of the protein repertoire
-
Chothia C, Gough J, Vogel C, Teichmann SA. Evolution of the protein repertoire. Science (New York, NY 2003, 300(5626):1701-1703.
-
(2003)
Science (New York, NY
, vol.300
, Issue.5626
, pp. 1701-1703
-
-
Chothia, C.1
Gough, J.2
Vogel, C.3
Teichmann, S.A.4
-
4
-
-
0032885169
-
Genome evolution and the evolution of exon-shuffling--a review
-
10.1016/S0378-1119(99)00228-0, 10570989
-
Patthy L. Genome evolution and the evolution of exon-shuffling--a review. Gene 1999, 238(1):103-114. 10.1016/S0378-1119(99)00228-0, 10570989.
-
(1999)
Gene
, vol.238
, Issue.1
, pp. 103-114
-
-
Patthy, L.1
-
5
-
-
61649112657
-
Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer
-
10.1016/j.jmb.2008.12.045, 19135455
-
Addou S, Rentzsch R, Lee D, Orengo CA. Domain-based and family-specific sequence identity thresholds increase the levels of reliable protein function transfer. Journal of molecular biology 2009, 387(2):416-430. 10.1016/j.jmb.2008.12.045, 19135455.
-
(2009)
Journal of molecular biology
, vol.387
, Issue.2
, pp. 416-430
-
-
Addou, S.1
Rentzsch, R.2
Lee, D.3
Orengo, C.A.4
-
6
-
-
84860848426
-
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation
-
bar068
-
Burge S, Kelly E, Lonsdale D, Mutowo-Muellenet P, McAnulla C, Mitchell A, Sangrador-Vegas A, Yong SY, Mulder N, Hunter S. Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database (Oxford) 2012, 2012:bar068.
-
(2012)
Database (Oxford)
, vol.2012
-
-
Burge, S.1
Kelly, E.2
Lonsdale, D.3
Mutowo-Muellenet, P.4
McAnulla, C.5
Mitchell, A.6
Sangrador-Vegas, A.7
Yong, S.Y.8
Mulder, N.9
Hunter, S.10
-
7
-
-
58149203231
-
InterPro: the integrative protein signature database
-
10.1093/nar/gkn785, 2686546, 18940856
-
Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al. InterPro: the integrative protein signature database. Nucleic acids research 2009, 37(Database):D211-215. 10.1093/nar/gkn785, 2686546, 18940856.
-
(2009)
Nucleic acids research
, vol.37
, Issue.DATABASE
-
-
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
-
8
-
-
78651285748
-
CDD: a Conserved Domain Database for the functional annotation of proteins
-
10.1093/nar/gkq1189, 3013737, 21109532
-
Marchler-Bauer A, Lu S, Anderson JB, Chitsaz F, Derbyshire MK, DeWeese-Scott C, Fong JH, Geer LY, Geer RC, Gonzales NR, et al. CDD: a Conserved Domain Database for the functional annotation of proteins. Nucleic acids research 2011, 39(Database):D225-229. 10.1093/nar/gkq1189, 3013737, 21109532.
-
(2011)
Nucleic acids research
, vol.39
, Issue.DATABASE
-
-
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
-
9
-
-
0030925920
-
Pfam: a comprehensive database of protein domain families based on seed alignments
-
10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L, 9223186
-
Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins 1997, 28(3):405-420. 10.1002/(SICI)1097-0134(199707)28:3<405::AID-PROT10>3.0.CO;2-L, 9223186.
-
(1997)
Proteins
, vol.28
, Issue.3
, pp. 405-420
-
-
Sonnhammer, E.L.1
Eddy, S.R.2
Durbin, R.3
-
10
-
-
0036228634
-
Predicting gene ontology functions from ProDom and CDD protein domains
-
10.1101/gr.222902, 187511, 11932249
-
Schug J, Diskin S, Mazzarelli J, Brunk BP, Stoeckert CJ. Predicting gene ontology functions from ProDom and CDD protein domains. Genome research 2002, 12(4):648-655. 10.1101/gr.222902, 187511, 11932249.
-
(2002)
Genome research
, vol.12
, Issue.4
, pp. 648-655
-
-
Schug, J.1
Diskin, S.2
Mazzarelli, J.3
Brunk, B.P.4
Stoeckert, C.J.5
-
11
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
-
10.1093/nar/25.17.3389, 146917, 9254694
-
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 1997, 25(17):3389-3402. 10.1093/nar/25.17.3389, 146917, 9254694.
-
(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
-
12
-
-
15944404663
-
Gotrees: predicting go associations from protein domain composition using decision trees
-
Hayete B, Bienkowska JR. Gotrees: predicting go associations from protein domain composition using decision trees. Pacific Symposium on Biocomputing 2005, 127-138.
-
(2005)
Pacific Symposium on Biocomputing
, pp. 127-138
-
-
Hayete, B.1
Bienkowska, J.R.2
-
14
-
-
68049117332
-
Gene ontology functional annotations at the structural domain level
-
10.1002/prot.22373, 19241468
-
Lopez D, Pazos F. Gene ontology functional annotations at the structural domain level. Proteins 2009, 76(3):598-607. 10.1002/prot.22373, 19241468.
-
(2009)
Proteins
, vol.76
, Issue.3
, pp. 598-607
-
-
Lopez, D.1
Pazos, F.2
-
15
-
-
0141742293
-
PANTHER: a library of protein families and subfamilies indexed by function
-
10.1101/gr.772403, 403709, 12952881
-
Thomas PD, Campbell MJ, Kejariwal A, Mi H, Karlak B, Daverman R, Diemer K, Muruganujan A, Narechania A. PANTHER: a library of protein families and subfamilies indexed by function. Genome research 2003, 13(9):2129-2141. 10.1101/gr.772403, 403709, 12952881.
-
(2003)
Genome research
, vol.13
, Issue.9
, pp. 2129-2141
-
-
Thomas, P.D.1
Campbell, M.J.2
Kejariwal, A.3
Mi, H.4
Karlak, B.5
Daverman, R.6
Diemer, K.7
Muruganujan, A.8
Narechania, A.9
-
16
-
-
0037249633
-
The TIGRFAMs database of protein families
-
10.1093/nar/gkg128, 165575, 12520025
-
Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic acids research 2003, 31(1):371-373. 10.1093/nar/gkg128, 165575, 12520025.
-
(2003)
Nucleic acids research
, vol.31
, Issue.1
, pp. 371-373
-
-
Haft, D.H.1
Selengut, J.D.2
White, O.3
-
17
-
-
0030777303
-
CATH--a hierarchic classification of protein domain structures
-
10.1016/S0969-2126(97)00260-8, 9309224
-
Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH--a hierarchic classification of protein domain structures. Structure 1997, 5(8):1093-1108. 10.1016/S0969-2126(97)00260-8, 9309224.
-
(1997)
Structure
, vol.5
, Issue.8
, pp. 1093-1108
-
-
Orengo, C.A.1
Michie, A.D.2
Jones, S.3
Jones, D.T.4
Swindells, M.B.5
Thornton, J.M.6
-
18
-
-
0036005911
-
Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database
-
10.1101/gr.213802, 155287, 11875040
-
Buchan DW, Shepherd AJ, Lee D, Pearl FM, Rison SC, Thornton JM, Orengo CA. Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. Genome research 2002, 12(3):503-514. 10.1101/gr.213802, 155287, 11875040.
-
(2002)
Genome research
, vol.12
, Issue.3
, pp. 503-514
-
-
Buchan, D.W.1
Shepherd, A.J.2
Lee, D.3
Pearl, F.M.4
Rison, S.C.5
Thornton, J.M.6
Orengo, C.A.7
-
19
-
-
77950362058
-
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains
-
10.1093/nar/gkp1049, 2817468, 19923231
-
Lee DA, Rentzsch R, Orengo C. GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic acids research 2010, 38(3):720-737. 10.1093/nar/gkp1049, 2817468, 19923231.
-
(2010)
Nucleic acids research
, vol.38
, Issue.3
, pp. 720-737
-
-
Lee, D.A.1
Rentzsch, R.2
Orengo, C.3
-
20
-
-
0034069495
-
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium
-
10.1038/75556, 3037419, 10802651
-
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
-
(2000)
Nature genetics
, vol.25
, Issue.1
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.P.7
Dolinski, K.8
Dwight, S.S.9
Eppig, J.T.10
-
21
-
-
84862192725
-
The UniProt-GO Annotation database in 2011
-
3245010, 22123736
-
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, et al. The UniProt-GO Annotation database in 2011. Nucleic acids research 2012, 40(Database):D565-570. 3245010, 22123736.
-
(2012)
Nucleic acids research
, vol.40
, Issue.DATABASE
-
-
Dimmer, E.C.1
Huntley, R.P.2
Alam-Faruque, Y.3
Sawford, T.4
O'Donovan, C.5
Martin, M.J.6
Bely, B.7
Browne, P.8
Mun Chan, W.9
Eberhardt, R.10
-
22
-
-
84860833500
-
Reorganizing the protein space at the Universal Protein Resource (UniProt)
-
3245120, 22102590
-
Consortium TU. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic acids research 2012, 40(Database):D71-75. 3245120, 22102590.
-
(2012)
Nucleic acids research
, vol.40
, Issue.DATABASE
-
-
Consortium, T.U.1
-
23
-
-
33947311528
-
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
-
10.1186/1471-2105-6-S1-S17, 1866391, 16351743
-
Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R. An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC bioinformatics 2005, 6(Suppl 1):S17. 10.1186/1471-2105-6-S1-S17, 1866391, 16351743.
-
(2005)
BMC bioinformatics
, vol.6
, Issue.SUPPL. 1
-
-
Camon, E.B.1
Barrell, D.G.2
Dimmer, E.C.3
Lee, V.4
Magrane, M.5
Maslen, J.6
Binns, D.7
Apweiler, R.8
-
24
-
-
0035872768
-
Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics
-
10.1006/geno.2001.6513, 11374909
-
Hill DP, Davis AP, Richardson JE, Corradi JP, Ringwald M, Eppig JT, Blake JA. Program description: Strategies for biological annotation of mammalian systems: implementing gene ontologies in mouse genome informatics. Genomics 2001, 74(1):121-128. 10.1006/geno.2001.6513, 11374909.
-
(2001)
Genomics
, vol.74
, Issue.1
, pp. 121-128
-
-
Hill, D.P.1
Davis, A.P.2
Richardson, J.E.3
Corradi, J.P.4
Ringwald, M.5
Eppig, J.T.6
Blake, J.A.7
-
25
-
-
84863693531
-
Quality of computationally inferred gene ontology annotations
-
10.1371/journal.pcbi.1002533, 3364937, 22693439
-
Skunca N, Altenhoff A, Dessimoz C. Quality of computationally inferred gene ontology annotations. PLoS computational biology 2012, 8(5):e1002533. 10.1371/journal.pcbi.1002533, 3364937, 22693439.
-
(2012)
PLoS computational biology
, vol.8
, Issue.5
-
-
Skunca, N.1
Altenhoff, A.2
Dessimoz, C.3
-
26
-
-
0003410183
-
Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes
-
Academic Press
-
Webb EC. Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes. 1992, Academic Press.
-
(1992)
-
-
Webb, E.C.1
-
27
-
-
33745634395
-
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 (Oxford, England) 2006, 22(13):1658-1659.
-
(2006)
Bioinformatics (Oxford, England)
, vol.22
, Issue.13
, pp. 1658-1659
-
-
Li, W.1
Godzik, A.2
-
28
-
-
80055082271
-
Accelerated Profile HMM Searches
-
10.1371/journal.pcbi.1002195, 3197634, 22039361
-
Eddy SR. Accelerated Profile HMM Searches. PLoS computational biology 2011, 7(10):e1002195. 10.1371/journal.pcbi.1002195, 3197634, 22039361.
-
(2011)
PLoS computational biology
, vol.7
, Issue.10
-
-
Eddy, S.R.1
-
29
-
-
77951946371
-
A fast and automated solution for accurately resolving protein domain architectures
-
Yeats C, Redfern OC, Orengo C. A fast and automated solution for accurately resolving protein domain architectures. Bioinformatics (Oxford, England) 2010, 26(6):745-751.
-
(2010)
Bioinformatics (Oxford, England)
, vol.26
, Issue.6
, pp. 745-751
-
-
Yeats, C.1
Redfern, O.C.2
Orengo, C.3
-
30
-
-
13244268370
-
GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes
-
10.1186/1471-2105-5-178, 535938, 15550167
-
Martin DM, Berriman M, Barton GJ. GOtcha: a new method for prediction of protein function assessed by the annotation of seven genomes. BMC bioinformatics 2004, 5:178. 10.1186/1471-2105-5-178, 535938, 15550167.
-
(2004)
BMC bioinformatics
, vol.5
, pp. 178
-
-
Martin, D.M.1
Berriman, M.2
Barton, G.J.3
-
31
-
-
59849089151
-
PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data
-
10.1002/prot.22172, 18655063
-
Hawkins T, Chitale M, Luban S, Kihara D. PFP: Automated prediction of gene ontology functional annotations with confidence scores using protein sequence data. Proteins 2009, 74(3):566-582. 10.1002/prot.22172, 18655063.
-
(2009)
Proteins
, vol.74
, Issue.3
, pp. 566-582
-
-
Hawkins, T.1
Chitale, M.2
Luban, S.3
Kihara, D.4
-
32
-
-
67649868148
-
ESG: extended similarity group method for automated protein function prediction
-
Chitale M, Hawkins T, Park C, Kihara D. ESG: extended similarity group method for automated protein function prediction. Bioinformatics (Oxford, England) 2009, 25(14):1739-1745.
-
(2009)
Bioinformatics (Oxford, England)
, vol.25
, Issue.14
, pp. 1739-1745
-
-
Chitale, M.1
Hawkins, T.2
Park, C.3
Kihara, D.4
-
33
-
-
0037423702
-
COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance
-
10.1016/S0022-2836(02)01371-2, 12547212
-
Sadreyev R, Grishin N. COMPASS: a tool for comparison of multiple protein alignments with assessment of statistical significance. Journal of molecular biology 2003, 326(1):317-336. 10.1016/S0022-2836(02)01371-2, 12547212.
-
(2003)
Journal of molecular biology
, vol.326
, Issue.1
, pp. 317-336
-
-
Sadreyev, R.1
Grishin, N.2
|