-
1
-
-
0346494941
-
SCOP database in 2004: Refinements integrate structure and sequence family data
-
Andreeva, A., Howorth, D., Brenner, S.E., Hubbard, T.J., Chothia, C., and Murzin, A.G. 2004. SCOP database in 2004: Refinements integrate structure and sequence family data. Nucleic Acids Res. 32:D226-D229.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Andreeva, A.1
Howorth, D.2
Brenner, S.E.3
Hubbard, T.J.4
Chothia, C.5
Murzin, A.G.6
-
2
-
-
0037248869
-
PRINTS and its automatic supplement, prePRINTS
-
Attwood, T.K., Bradley, P., Flower, D.R., Gaulton, A., Maudling, N., Mitchell, A.L., Moulton, G., Nordle, A., Paine, K., Taylor, P., Uddin, A., and Zygouri, C. 2003. PRINTS and its automatic supplement, prePRINTS. Nucleic Acids Res. 31:400-402.
-
(2003)
Nucleic Acids Res
, vol.31
, 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
-
3
-
-
13444305296
-
The ProDom database of protein domain families: More emphasis on 3D
-
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 Rese. 33:D212-D215.
-
(2005)
Nucleic Acids Rese
, vol.33
-
-
Bru, C.1
Courcelle, E.2
Carrere, S.3
Beausse, Y.4
Dalmar, S.5
Kahn, D.6
-
4
-
-
0033957841
-
ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons
-
Corpet, F., Servant, F., Gouzy, J., and Kahn, D. 2000. ProDom and ProDom-CG: Tools for protein domain analysis and whole genome comparisons. Nucleic Acids Res. 28:267-269.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 267-269
-
-
Corpet, F.1
Servant, F.2
Gouzy, J.3
Kahn, D.4
-
5
-
-
0031743421
-
-
Available online as HMMER2 Profile hidden Markov models for biological sequence analysis;
-
Eddy, S.R. 1998. Profile hidden Markov models. Bioinformatics 14:755-763. (Available online as HMMER2 Profile hidden Markov models for biological sequence analysis; http://hmmer.janelia.org.)
-
(1998)
Profile hidden Markov models. Bioinformatics
-
-
Eddy, S.R.1
-
6
-
-
33644876020
-
Pfam: Clans, web tools and services
-
Finn, R.D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R., Eddy, S.R., Sonnhammer, E.L., and Bateman, A. 2006. Pfam: Clans, web tools and services. Nucleic Acids Res. 34:D247-D251.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Finn, R.D.1
Mistry, J.2
Schuster-Bockler, B.3
Griffiths-Jones, S.4
Hollich, V.5
Lassmann, T.6
Moxon, S.7
Marshall, M.8
Khanna, A.9
Durbin, R.10
Eddy, S.R.11
Sonnhammer, E.L.12
Bateman, A.13
-
7
-
-
33644875286
-
The Gene Ontology (GO) project in 2006
-
The Gene Ontology Consortium
-
The Gene Ontology Consortium. 2006. The Gene Ontology (GO) project in 2006. Nucleic Acids Res. 34:D322-D326.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
-
8
-
-
33846033844
-
The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution
-
Greene, L.H., Lewis, T.E., Addou, S., Cuff, A., Dallman, T., Dibley, M., Redfern, O., Pearl, F., Nambudiry, R., Reid, A., Sillitoe, I., Yeats, C., Thornton, J.M., and Orengo, C.A. 2007. The CATH domain structure database: New protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res. 35:D291-D297.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Greene, L.H.1
Lewis, T.E.2
Addou, S.3
Cuff, A.4
Dallman, T.5
Dibley, M.6
Redfern, O.7
Pearl, F.8
Nambudiry, R.9
Reid, A.10
Sillitoe, I.11
Yeats, C.12
Thornton, J.M.13
Orengo, C.A.14
-
9
-
-
33644876022
-
The PROSITE database
-
Hulo, N., Bairoch, A., Bulliard, V., Cerutti, L., De Castro, E., Langendijk-Genevaux, P.S., Pagni, M., and Sigrist, C.J.A. 2006. The PROSITE database. Nucleic Acids Res. 34:D227-D230.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Hulo, N.1
Bairoch, A.2
Bulliard, V.3
Cerutti, L.4
De Castro, E.5
Langendijk-Genevaux, P.S.6
Pagni, M.7
Sigrist, C.J.A.8
-
10
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
International Human Genome Consortium
-
International Human Genome Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409:860-921.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
-
11
-
-
0036184726
-
Interactive InterPro-based comparisons of proteins in whole genomes
-
Kanapin, A., Apweiler, R., Biswas, M., Fleischmann, W., Karavidopoulou, Y., Kersey, P., Kriventseva, E.V., Mittard, V., Mulder, N., Oinn, T., Phan, I., Servant, F., and Zdobnov, E. 2002. Interactive InterPro-based comparisons of proteins in whole genomes. Bioinformatics 18:374-375.
-
(2002)
Bioinformatics
, vol.18
, pp. 374-375
-
-
Kanapin, A.1
Apweiler, R.2
Biswas, M.3
Fleischmann, W.4
Karavidopoulou, Y.5
Kersey, P.6
Kriventseva, E.V.7
Mittard, V.8
Mulder, N.9
Oinn, T.10
Phan, I.11
Servant, F.12
Zdobnov, E.13
-
12
-
-
13444304365
-
Integr8 and genome reviews: Integrated views of complete genomes and proteomes
-
Kersey P., Bower, L., Morris, L., Horne, A., Petryszak, R., Kanz, C., Kanapin, A., Das, U., Michoud, K., Phan, I., Gattiker, A.,Kulikova, T., Faruque, N., Duggan, K., Mclaren, P., Reimholz, B., Duret, L., Penel, S., Reuter, I., and Apweiler, R. 2005 Integr8 and genome reviews: Integrated views of complete genomes and proteomes. Nucleic Acids Res. 33:D297-D302.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Kersey, P.1
Bower, L.2
Morris, L.3
Horne, A.4
Petryszak, R.5
Kanz, C.6
Kanapin, A.7
Das, U.8
Michoud, K.9
Phan, I.10
Gattiker, A.11
Kulikova, T.12
Faruque, N.13
Duggan, K.14
Mclaren, P.15
Reimholz, B.16
Duret, L.17
Penel, S.18
Reuter, I.19
Apweiler, R.20
more..
-
13
-
-
33644874606
-
The SWISS-MODEL repository: New features and functionalities
-
Kopp, J. and Schwede, T. 2006. The SWISS-MODEL repository: New features and functionalities. Nucleic Acids Res. 34:D315-D318.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kopp, J.1
Schwede, T.2
-
14
-
-
33644873706
-
The RCSB PDB information portal for structural genomics
-
Kouranov, A., Xie, L., de la Cruz, J., Chen, L., Westbrook, J., Bourne, P.E., and Berman, H.M. 2006. The RCSB PDB information portal for structural genomics. Nucleic Acids Res. 34:D302-D305.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Kouranov, A.1
Xie, L.2
de la Cruz, J.3
Chen, L.4
Westbrook, J.5
Bourne, P.E.6
Berman, H.M.7
-
15
-
-
0035910270
-
Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes
-
Krogh, A., Larsson, B., von Heijne, G., and Sonnhammer, E.L. 2001. Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol. 305:567-580.
-
(2001)
J. Mol. Biol
, vol.305
, pp. 567-580
-
-
Krogh, A.1
Larsson, B.2
von Heijne, G.3
Sonnhammer, E.L.4
-
16
-
-
33644877451
-
SMART 5: Domains in the context of genomes and networks
-
Letunic, I., Copley, R.R., Pils, B., Pinkert, S., Schultz, J., and Bork, P. 2006. SMART 5: Domains in the context of genomes and networks. Nucleic Acids Res. 34:D257-D260.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Letunic, I.1
Copley, R.R.2
Pils, B.3
Pinkert, S.4
Schultz, J.5
Bork, P.6
-
17
-
-
33846067524
-
PANTHER version 6: Protein sequence and function evolution data with expanded representation of biological pathways
-
Mi, H., Guo, N., Kejariwal, A., and Thomas, P.D. 2007. PANTHER version 6: Protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res. 35:D247-D252.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Mi, H.1
Guo, N.2
Kejariwal, A.3
Thomas, P.D.4
-
18
-
-
33846116032
-
-
Mulder,N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Buillard, V., Cerutti, L., Copley, R., Courcelle, E., Das, U., Daugherty, L., Dibley, M., Finn, R., Fleischmann, W., Gough, J., Haft, D., Hulo, N., Hunter, S., Kahn, D., Kanapin, A., Kejariwal, A., Labarga, A., Langendijk-Genevaux, P.S., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J.D., Sigrist, C.J., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H., and Yeats, C. 2007. New developments in the InterPro database. Nucleic Acids Res. 35:D224-D228.
-
Mulder,N.J., Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Buillard, V., Cerutti, L., Copley, R., Courcelle, E., Das, U., Daugherty, L., Dibley, M., Finn, R., Fleischmann, W., Gough, J., Haft, D., Hulo, N., Hunter, S., Kahn, D., Kanapin, A., Kejariwal, A., Labarga, A., Langendijk-Genevaux, P.S., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A.N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J.D., Sigrist, C.J., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H., and Yeats, C. 2007. New developments in the InterPro database. Nucleic Acids Res. 35:D224-D228.
-
-
-
-
19
-
-
0031240609
-
A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites
-
Nielsen, H., Engelbrecht, J., Brunak, S., and von Heijne, G. 1997. A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Int. J. Neural. Syst. 8:581-599.
-
(1997)
Int. J. Neural. Syst
, vol.8
, pp. 581-599
-
-
Nielsen, H.1
Engelbrecht, J.2
Brunak, S.3
von Heijne, G.4
-
20
-
-
33644874394
-
MODBASE: A database of annotated comparative protein structure models and associated resources
-
Pieper, U., Eswar, N., Davis, F.P., Braberg, H., Madhusudhan, M.S., Rossi, A., Marti-Renom, M., Karchin, R., Webb, B.M., Eramian, D., Shen, M.Y., Kelly, L., Melo, F., and Sali, A. 2006. MODBASE: A database of annotated comparative protein structure models and associated resources. Nucleic Acids Res. 34:D291-295.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Pieper, U.1
Eswar, N.2
Davis, F.P.3
Braberg, H.4
Madhusudhan, M.S.5
Rossi, A.6
Marti-Renom, M.7
Karchin, R.8
Webb, B.M.9
Eramian, D.10
Shen, M.Y.11
Kelly, L.12
Melo, F.13
Sali, A.14
-
21
-
-
23144458473
-
InterProScan: Protein domains identifier
-
Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., and Lopez, R. 2005. InterProScan: Protein domains identifier. Nucleic Acids Res. 33:W116-W120.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Quevillon, E.1
Silventoinen, V.2
Pillai, S.3
Harte, N.4
Mulder, N.5
Apweiler, R.6
Lopez, R.7
-
22
-
-
0033388381
-
FingerPRINTScan: Intelligent searching of the PRINTS motif database
-
Scordis, P., Flower, D.R., and Attwood, T.K. 1999. FingerPRINTScan: Intelligent searching of the PRINTS motif database. Bioinformatics 15:799-806.
-
(1999)
Bioinformatics
, vol.15
, pp. 799-806
-
-
Scordis, P.1
Flower, D.R.2
Attwood, T.K.3
-
23
-
-
33846113652
-
TIGRFAMs and Genome Properties: Tools for the assignment of molecular function and biological process in prokaryotic genomes
-
Selengut, J.D., Haft, D.H., Davidsen, T., Ganapathy, A., Gwinn-Giglio, M., Nelson, W.C., Richter, A.R., and White, O. 2007. TIGRFAMs and Genome Properties: Tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 35:D260-D264.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Selengut, J.D.1
Haft, D.H.2
Davidsen, T.3
Ganapathy, A.4
Gwinn-Giglio, M.5
Nelson, W.C.6
Richter, A.R.7
White, O.8
-
24
-
-
33846041078
-
The Universal Protein Resource (UniProt)
-
The UniProt Consortium
-
The UniProt Consortium. 2007. The Universal Protein Resource (UniProt). Nucleic Acids Res. 35:D193-D197.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
-
25
-
-
33846044585
-
The SUPERFAMILY database in 2007: Families and functions
-
Wilson, D., Madera, M., Vogel, C., Chothia, C., and Gough, J. 2007. The SUPERFAMILY database in 2007: Families and functions. Nucleic Acids Res. 35:D308-D313.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Wilson, D.1
Madera, M.2
Vogel, C.3
Chothia, C.4
Gough, J.5
-
26
-
-
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., Ledley, R.S., Suzek, B.E., Arminski, L., Chen, Y., Zhang, J., Cardenas, J.L., Chung, S., Castro-Alvear, J., Dinkov, G., and Barker, W.C. 2004. PIRSF: Family classification system at the Protein Information Resource. Nucleic Acids Res. 32:D112-D114.
-
(2004)
Nucleic Acids Res
, vol.32
-
-
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..
-
27
-
-
33644873932
-
Gene3D: Modelling protein structure, function and evolution
-
Yeats, C., Maibaum, M., Marsden, R., Dibley, M., Lee, D., Addou, S., and Orengo, C.A. 2006. Gene3D: Modelling protein structure, function and evolution. Nucleic Acids Res. 34:D281-284.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Yeats, C.1
Maibaum, M.2
Marsden, R.3
Dibley, M.4
Lee, D.5
Addou, S.6
Orengo, C.A.7
-
28
-
-
0036677719
-
The EBI SRS server-new features
-
Zdobnov, E.M., Lopez, R., Apweiler, R., and Etzold, T. 2002. The EBI SRS server-new features. Bioinformatics 18:1149-1150.
-
(2002)
Bioinformatics
, vol.18
, pp. 1149-1150
-
-
Zdobnov, E.M.1
Lopez, R.2
Apweiler, R.3
Etzold, T.4
|