DIMA


21097782	DIMA 3.0: Domain Interaction Map. [PMID: 21097782] Luo Q, Pagel P, Vilne B, Frishman D. Abstract Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software. Nucleic Acids Res. 2011:39(Database issue) \| 24 Citations (from Europe PMC, 2025-03-15)
17999995	DIMA 2.0--predicted and known domain interactions. [PMID: 17999995] Pagel P, Oesterheld M, Tovstukhina O, Strack N, Stümpflen V, Frishman D. 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. Nucleic Acids Res. 2008:36(Database issue) \| 8 Citations (from Europe PMC, 2025-03-15)
16481337	The DIMA web resource--exploring the protein domain network. [PMID: 16481337] Pagel P, Oesterheld M, Stümpflen V, Frishman D. Abstract Conserved domains represent essential building blocks of most known proteins. Owing to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria. http://mips.gsf.de/genre/proj/dima Bioinformatics. 2006:22(8) \| 11 Citations (from Europe PMC, 2025-03-15)

DIMA 3.0: Domain Interaction Map. [PMID: 21097782]

Luo Q, Pagel P, Vilne B, Frishman D.

Domain Interaction MAp (DIMA, available at http://webclu.bio.wzw.tum.de/dima) is a database of predicted and known interactions between protein domains. It integrates 5807 structurally known interactions imported from the iPfam and 3did databases and 46,900 domain interactions predicted by four computational methods: domain phylogenetic profiling, domain pair exclusion algorithm correlated mutations and domain interaction prediction in a discriminative way. Additionally predictions are filtered to exclude those domain pairs that are reported as non-interacting by the Negatome database. The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software.

Nucleic Acids Res. 2011:39(Database issue) | 24 Citations (from Europe PMC, 2025-03-15)

DIMA 2.0--predicted and known domain interactions. [PMID: 17999995]

Pagel P, Oesterheld M, Tovstukhina O, Strack N, Stümpflen V, Frishman D.

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.

Nucleic Acids Res. 2008:36(Database issue) | 8 Citations (from Europe PMC, 2025-03-15)

The DIMA web resource--exploring the protein domain network. [PMID: 16481337]

Pagel P, Oesterheld M, Stümpflen V, Frishman D.

Abstract

Conserved domains represent essential building blocks of most known proteins. Owing to their role as modular components carrying out specific functions they form a network based both on functional relations and direct physical interactions. We have previously shown that domain interaction networks provide substantially novel information with respect to networks built on full-length protein chains. In this work we present a comprehensive web resource for exploring the Domain Interaction MAp (DIMA), interactively. The tool aims at integration of multiple data sources and prediction techniques, two of which have been implemented so far: domain phylogenetic profiling and experimentally demonstrated domain contacts from known three-dimensional structures. A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria. http://mips.gsf.de/genre/proj/dima

Bioinformatics. 2006:22(8) | 11 Citations (from Europe PMC, 2025-03-15)

URL:	http://webclu.bio.wzw.tum.de/dima
Full name:	Domain Interaction MAp
Description:	DIMA is a Domain Interaction MAp and aims at becoming a comprehensive resource for functional and physical interactions among conserved protein-domains. The scope of the resource comprises both experimental data and computational predictions. Several methods and datasets have been integrated, already and inclusion of others is under way.
Year founded:	2006
Last update:	NA
Version:	v3.0
Accessibility:	Accessible
Country/Region:	Germany

Data type:	Protein
Data object:	NA
Database category:	Interaction
Major species:	NA
Keywords:	conserved protein-domain protein-protein interaction

University/Institution:	Technical University of Munich
Address:	The Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
City:	Freising
Province/State:
Country/Region:	Germany
Contact name (PI/Team):	Dmitrij Frishman
Contact email (PI/Helpdesk):	d.frishman@wzw.tum.de

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Database Commons a catalog of worldwide biological databases