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DIMA 2.0--predicted and known domain interactions.

Pagel P, Oesterheld M, Tovstukhina O, Strack N, Stümpflen V, Frishman D - Nucleic Acids Res. (2007)

Bottom Line: With this update, DIMA obtains greatly improved coverage at the level of genomes and domains as well as with respect to available prediction approaches.Experimental data comes from iPfam (3074) and 3did (3034 pairs), two databases identifying domain contacts in solved protein structures.Taken together, these two resources yielded 3653 distinct interacting domain pairs.

View Article: PubMed Central - PubMed

Affiliation: Lehrstuhl für Genomorientierte Bioinformatik, Wissenschaftszentrum Weihenstephan, Technische Universität München, Am Forum 1, D-85350 Freising, Germany. p.pagel@wzw.tum.de

ABSTRACT
DIMA-the domain interaction map has evolved from a simple web server for domain phylogenetic profiling into an integrative prediction resource combining both experimental data on domain-domain interactions and predictions from two different algorithms. With this update, DIMA obtains greatly improved coverage at the level of genomes and domains as well as with respect to available prediction approaches. The domain phylogenetic profiling method now uses SIMAP as its backend for exhaustive domain hit coverage: 7038 Pfam domains were profiled over 460 completely sequenced genomes. Domain pair exclusion predictions were produced from 83 969 distinct protein-protein interactions obtained from IntAct resulting in 21 513 domain pairs with significant domain pair exclusion algorithm scores. Additional predictions applying the same algorithm to predicted protein interactions from STRING yielded 2378 high-confidence pairs. Experimental data comes from iPfam (3074) and 3did (3034 pairs), two databases identifying domain contacts in solved protein structures. Taken together, these two resources yielded 3653 distinct interacting domain pairs. DIMA is available at http://mips.gsf.de/genre/proj/dima.

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If desired, a graphical representation of the local domain neighborhood is shown.
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Figure 2: If desired, a graphical representation of the local domain neighborhood is shown.

Mentions: Results are primarily presented in a concise table format (Figure 1) showing the predictions and data sources supporting the domain relations and the user can choose to view a graphical representation of the local domain neighborhood (Figure 2) or details on the domain phylogenetic profiling results (Figure 3). The network can be navigated by centering any domain in the neighborhood and re-computing its respective interactions.Figure 1.


DIMA 2.0--predicted and known domain interactions.

Pagel P, Oesterheld M, Tovstukhina O, Strack N, Stümpflen V, Frishman D - Nucleic Acids Res. (2007)

If desired, a graphical representation of the local domain neighborhood is shown.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238836&req=5

Figure 2: If desired, a graphical representation of the local domain neighborhood is shown.
Mentions: Results are primarily presented in a concise table format (Figure 1) showing the predictions and data sources supporting the domain relations and the user can choose to view a graphical representation of the local domain neighborhood (Figure 2) or details on the domain phylogenetic profiling results (Figure 3). The network can be navigated by centering any domain in the neighborhood and re-computing its respective interactions.Figure 1.

Bottom Line: With this update, DIMA obtains greatly improved coverage at the level of genomes and domains as well as with respect to available prediction approaches.Experimental data comes from iPfam (3074) and 3did (3034 pairs), two databases identifying domain contacts in solved protein structures.Taken together, these two resources yielded 3653 distinct interacting domain pairs.

View Article: PubMed Central - PubMed

Affiliation: Lehrstuhl für Genomorientierte Bioinformatik, Wissenschaftszentrum Weihenstephan, Technische Universität München, Am Forum 1, D-85350 Freising, Germany. p.pagel@wzw.tum.de

ABSTRACT
DIMA-the domain interaction map has evolved from a simple web server for domain phylogenetic profiling into an integrative prediction resource combining both experimental data on domain-domain interactions and predictions from two different algorithms. With this update, DIMA obtains greatly improved coverage at the level of genomes and domains as well as with respect to available prediction approaches. The domain phylogenetic profiling method now uses SIMAP as its backend for exhaustive domain hit coverage: 7038 Pfam domains were profiled over 460 completely sequenced genomes. Domain pair exclusion predictions were produced from 83 969 distinct protein-protein interactions obtained from IntAct resulting in 21 513 domain pairs with significant domain pair exclusion algorithm scores. Additional predictions applying the same algorithm to predicted protein interactions from STRING yielded 2378 high-confidence pairs. Experimental data comes from iPfam (3074) and 3did (3034 pairs), two databases identifying domain contacts in solved protein structures. Taken together, these two resources yielded 3653 distinct interacting domain pairs. DIMA is available at http://mips.gsf.de/genre/proj/dima.

Show MeSH