Showing Publication Results for :

3DID
Full Name of the Resource : 3D interacting domains: Domain-domain interactions in proteins with known 3D structures
Resource Category : Databases -> Metabolic and Signaling Pathways -> Protein-Protein Interactions

  1. Title of the Paper : 3did Update: domain-domain and peptide-mediated interactions of known 3D structure (View at PubMed)
    Contributors : Stein, A.; Panjkovich, A.; Aloy, P.
    Address : Institute for Research in Biomedicine, Barcelona Supercomputing Center, c/ Baldiri Reixac 10-12, 08028 Barcelona, Spain.
    Publication Name : Nucleic Acids Res
    Volume : 37
    Issue : Database issue
    Pages : D300-4
    Publication Year : 2009
    ISSN : 1362-4962 (Electronic) 0305-1048 (Linking)
    Language : English
    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.



  2. Title of the Paper : 3did: identification and classification of domain-based interactions of known three-dimensional structure (View at PubMed)
    Contributors : Stein, A.; Ceol, A.; Aloy, P.
    Address : Institute for Research in Biomedicine, Join IRB-BSC Program in Computational Biology, 08028 Barcelona, Spain.
    Publication Name : Nucleic Acids Res
    Volume : 39
    Issue : Database issue
    Pages : D718-23
    ISSN : 1362-4962 (Electronic) 0305-1048 (Linking)
    Language : English
    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.



  3. Title of the Paper : 3did: interacting protein domains of known three-dimensional structure (View at PubMed)
    Contributors : Stein, A.; Russell, R. B.; Aloy, P.
    Address : EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
    Publication Name : Nucleic Acids Res
    Volume : 33
    Issue : Database issue
    Pages : D413-7
    Publication Year : 2005
    ISSN : 1362-4962 (Electronic) 0305-1048 (Linking)
    Language : English
    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.