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. 2005 Jan 1;33(Database issue):D212-5.
doi: 10.1093/nar/gki034.

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

Catherine Bru  1 , Emmanuel Courcelle, Sébastien Carrère, Yoann Beausse, Sandrine Dalmar, Daniel Kahn
Affiliations

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

Catherine Bru et al. Nucleic Acids Res. .

Abstract

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.

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Figures

Figure 1
Figure 1
Information, tools and links available for each ProDom domain family. (A) Tools and links, from left to right: domain arrangements for all proteins belonging to this family; corresponding family in ProDom-CG; family in the MSF or FASTA file formats; download PSI-BLAST generated profile; run Predict Protein on family (20); and family display enhanced with ESPript (21). (B) General information on domain family: most frequent protein names and descriptors, length of multiple sequence alignment, number of domains, consistency indicators (3) and norMD assessment of alignment quality (12). (C) Links to InterPro, PROSITE, PFAM-A and PDB. (D) Visualization of ProDom domains on 3D structure.
Figure 2
Figure 2
Domain arrangements of proteins in a ProDom family. (A) Proteins sharing the same domain architecture are grouped in order to simplify the output. This feature can be disabled to display a complete output. (B) String search in SWISS-PROT identifiers or accession numbers allows to highlight the corresponding proteins in the display. (C) Navigation bar to browse the output, with at most 200 different domain arrangements displayed in a single page. (D) The left icon on each line is linked to a display of all proteins sharing at least one homologous domain with the current protein. When relevant, another icon points to the list of all proteins sharing the same domain architecture. Domain cartoons are hypertext-linked to the corresponding ProDom domain families (Figure 1) whose accession number is also available on mouse-over together with a short description.
See this image and copyright information in PMC

References

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