Topic
3did
About: 3did is a research topic. Over the lifetime, 19 publications have been published within this topic receiving 969 citations.
Papers
TL;DR: The database of 3D interacting domains (3did), available online for browsing and bulk download at http://3did.irbbarcelona.org, is a reference source of information for the structural characterization of protein interaction networks.
Abstract: The database of 3D interacting domains (3did, available online for browsing and bulk download at http://3did.irbbarcelona.org) is a catalog of protein-protein interactions for which a high-resolution 3D structure is known. 3did collects and classifies all structural templates of domain-domain interactions in the Protein Data Bank, providing molecular details for such interactions. The current version also includes a pipeline for the discovery and annotation of novel domain-motif interactions. For every interaction, 3did identifies and groups different binding modes by clustering similar interfaces into 'interaction topologies'. By maintaining a constantly updated collection of domain-based structural interaction templates, 3did is a reference source of information for the structural characterization of protein interaction networks. 3did is updated every 6 months.
293 citations
TL;DR: The database of 3D Interacting Domains (3did) is a collection of domain–domain interactions in proteins for which high-resolution three-dimensional structures are known that offers an overview of how similar in structure are interactions between different members of the same protein family.
Abstract: The database of 3D Interacting Domains (3did) is a collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known. 3did exploits structural information to provide critical molecular details necessary for understanding how interactions occur. It also offers an overview of how similar in structure are interactions between different members of the same protein family. The database also contains Gene Ontology-based functional annotations and interactions between yeast proteins from large-scale interaction discovery studies. A web-based tool to query 3did is available at http://3did.embl.de.
205 citations
TL;DR: 3did exploits the availability of structural data to provide molecular details on interactions between two globular domains as well as novel domain–peptide interactions, derived using a recently published method from the lab.
Abstract: The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. 3did exploits the availability of structural data to provide molecular details on interactions between two globular domains as well as novel domain-peptide interactions, derived using a recently published method from our lab. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The 3did web server at http://3did.irbbarcelona.org visualizes these interfaces along with atomic details of individual interactions using Jmol. The complete contents are also available for download.
151 citations
TL;DR: The microbial protein interaction database (MPIDB) aims to collect and provide all known physical microbial interactions.
Abstract: Summary: The microbial protein interaction database (MPIDB) aims to collect and provide all known physical microbial interactions. Currently, 22 530 experimentally determined interactions among proteins of 191 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 24 060 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 8150 additional evidences based on interaction conservation, co-purification and 3D domain contacts (iPfam, 3did).
Availability: http://www.jcvi.org/mpidb/
Contact: gro.ivcj@llogj
132 citations
TL;DR: The database of 3D interacting domains (3did) is a collection of protein interactions for which high-resolution 3D structures are known that contains a hand-curated set of transient peptide-mediated interactions.
Abstract: The database of 3D interacting domains (3did) is a collection of protein interactions for which high-resolution 3D structures are known. 3did exploits structural information to provide the crucial molecular details necessary for understanding how protein interactions occur. Besides interactions between globular domains, the new release of 3did also contains a hand-curated set of transient peptide-mediated interactions. The interactions are grouped in Interaction Types, based on the mode of binding, and the different binding interfaces used in each type are also identified and catalogued. A web-based tool to query 3did is available at http://3did.irbbarcelona.org.
76 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2021 | 2 |
| 2016 | 1 |
| 2015 | 1 |
| 2014 | 2 |
| 2013 | 2 |
| 2012 | 1 |