Skip Navigation

Nucleic Acids Research 2005 33(Database Issue):D212-D215; doi:10.1093/nar/gki034
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (539K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Bru, C.
Right arrow Articles by Kahn, D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Bru, C.
Right arrow Articles by Kahn, D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2005, Vol. 33, Database issue D212-D215
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

The ProDom database of protein domain families: more emphasis on 3D

Catherine Bru, Emmanuel Courcelle, Sébastien Carrère, Yoann Beausse, Sandrine Dalmar and Daniel Kahn*

Laboratoire des Interactions Plantes-Microorganismes, INRA/CNRS, BP 27, F-31326 Castanet-Tolosan Cedex, France

* To whom correspondence should be addressed. Tel: +33 5 61 28 53 29; Fax: +33 5 61 28 50 61; Email: Daniel.Kahn{at}toulouse.inra.fr

Received September 15, 2004; Revised and Accepted September 23, 2004

ProDom is a comprehensive database of protein domain families generated from the global comparison of all available protein sequences. Recent improvements include the use of three-dimensional (3D) information from the SCOP database; a completely redesigned web interface (http://www.toulouse.inra.fr/prodom.html); visualization of ProDom domains on 3D structures; coupling of ProDom analysis with the Geno3D homology modelling server; Bayesian inference of evolutionary scenarios for ProDom families. In addition, we have developed ProDom-SG, a ProDom-based server dedicated to the selection of candidate proteins for structural genomics.

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
D. A. Lee, R. Rentzsch, and C. Orengo
GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains
Nucleic Acids Res., November 18, 2009; (2009) gkp1049v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Marsico, K. Scheubert, A. Tuukkanen, A. Henschel, C. Winter, R. Winnenburg, and M. Schroeder
MeMotif: a database of linear motifs in {alpha}-helical transmembrane proteins
Nucleic Acids Res., November 12, 2009; (2009) gkp1042v1.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
L. Huang, C. Cagnon, P. Caumette, and R. Duran
First Gene Cassettes of Integrons as Targets in Finding Adaptive Genes in Metagenomes
Appl. Envir. Microbiol., June 1, 2009; 75(11): 3823 - 3825.
[Abstract] [Full Text] [PDF]

Home page
 J R Soc InterfaceHome page
G. A Reeves, D. Talavera, and J. M Thornton
Genome and proteome annotation: organization, interpretation and integration
J R Soc Interface, February 6, 2009; 6(31): 129 - 147.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Hunter, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bork, U. Das, L. Daugherty, L. Duquenne, et al.
InterPro: the integrative protein signature database
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D211 - D215.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Bhasi, P. Philip, V. Manikandan, and P. Senapathy
ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D703 - D711.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
D. Wilson, R. Pethica, Y. Zhou, C. Talbot, C. Vogel, M. Madera, C. Chothia, and J. Gough
SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny
Nucleic Acids Res., January 1, 2009; 37(suppl_1): D380 - D386.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
H. Stockinger, T. Attwood, S. N. Chohan, R. Cote, P. Cudre-Mauroux, L. Falquet, P. Fernandes, R. D. Finn, T. Hupponen, E. Korpelainen, et al.
Experience using web services for biological sequence analysis
Brief Bioinform, November 1, 2008; 9(6): 493 - 505.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
S. Wong and M. A. Ragan
MACHOS: Markov clusters of homologous subsequences
Bioinformatics, July 1, 2008; 24(13): i77 - i85.
[Abstract] [Full Text] [PDF]

Home page
 Brief BioinformHome page
S. J. Sammut, R. D. Finn, and A. Bateman
Pfam 10 years on: 10 000 families and still growing
Brief Bioinform, May 1, 2008; 9(3): 210 - 219.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. D. Finn, J. Tate, J. Mistry, P. C. Coggill, S. J. Sammut, H.-R. Hotz, G. Ceric, K. Forslund, S. R. Eddy, E. L. L. Sonnhammer, et al.
The Pfam protein families database
Nucleic Acids Res., January 11, 2008; 36(suppl_1): D281 - D288.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
F. Beaussart, J. Weiner 3rd, and E. Bornberg-Bauer
Automated Improvement of Domain ANnotations using context analysis of domain arrangements (AIDAN)
Bioinformatics, July 15, 2007; 23(14): 1834 - 1836.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. E. Gewehr, V. Hintermair, and R. Zimmer
AutoSCOP: automated prediction of SCOP classifications using unique pattern-class mappings
Bioinformatics, May 15, 2007; 23(10): 1203 - 1210.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
G. Amoutzias, A. Veron, J Weiner III, M Robinson-Rechavi, E Bornberg-Bauer, S. Oliver, and D. Robertson
One Billion Years of bZIP Transcription Factor Evolution: Conservation and Change in Dimerization and DNA-Binding Site Specificity
Mol. Biol. Evol., March 1, 2007; 24(3): 827 - 835.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. J. Mulder, R. Apweiler, T. K. Attwood, A. Bairoch, A. Bateman, D. Binns, P. Bork, V. Buillard, L. Cerutti, R. Copley, et al.
New developments in the InterPro database
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D224 - D228.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. M. Phuong, C. B. Do, R. C. Edgar, and S. Batzoglou
Multiple alignment of protein sequences with repeats and rearrangements
Nucleic Acids Res., November 6, 2006; 34(20): 5932 - 5942.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Bryson, V. Loux, R. Bossy, P. Nicolas, S. Chaillou, M. van de Guchte, S. Penaud, E. Maguin, M. Hoebeke, P. Bessieres, et al.
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system
Nucleic Acids Res., July 19, 2006; 34(12): 3533 - 3545.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J.-H. Hung, H.-D. Huang, and T.-Y. Lee
ProKware: integrated software for presenting protein structural properties in protein tertiary structures.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W89 - W94.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
K. S. Makarova, E. V. Koonin, R. Haselkorn, and M. Y. Galperin
Cyanobacterial response regulator PatA contains a conserved N-terminal domain (PATAN) with an alpha-helical insertion
Bioinformatics, June 1, 2006; 22(11): 1297 - 1301.
[Abstract] [Full Text] [PDF]

Home page
 Hum Mol GenetHome page
G. A. Reeves, J. M. Thornton, and the BioSapiens Network of Excellence
Integrating biological data through the genome
Hum. Mol. Genet., April 15, 2006; 15(suppl_1): R81 - R87.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. L. Marsden, D. Lee, M. Maibaum, C. Yeats, and C. A. Orengo
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space
Nucleic Acids Res., February 15, 2006; 34(3): 1066 - 1080.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
M. Herzberg, I. K. Kaye, W. Peti, and T. K. Wood
YdgG (TqsA) Controls Biofilm Formation in Escherichia coli K-12 through Autoinducer 2 Transport
J. Bacteriol., January 15, 2006; 188(2): 587 - 598.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Tripathy, V. N. Pandey, B. Fang, F. Salas, and B. M. Tyler
VMD: a community annotation database for oomycetes and microbial genomes
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D379 - D381.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
S. Hartmann, D. Lu, J. Phillips, and T. J. Vision
Phytome: a platform for plant comparative genomics
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D724 - D730.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
E. Quevillon, V. Silventoinen, S. Pillai, N. Harte, N. Mulder, R. Apweiler, and R. Lopez
InterProScan: protein domains identifier
Nucleic Acids Res., July 1, 2005; 33(suppl_2): W116 - W120.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
V. Kunin, S. A. Teichmann, M. A. Huynen, and C. A. Ouzounis
The properties of protein family space depend on experimental design
Bioinformatics, June 1, 2005; 21(11): 2618 - 2622.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
S. B. Cannon, J. A. Crow, M. L. Heuer, X. Wang, E. K.S. Cannon, C. Dwan, A.-F. Lamblin, J. Vasdewani, J. Mudge, A. Cook, et al.
Databases and Information Integration for the Medicago truncatula Genome and Transcriptome
Plant Physiology, May 1, 2005; 138(1): 38 - 46.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.