Database Commons a catalog of biological databases

Database Commons - 3did

3did

Citations: 399

z-index 19.64

Short name 3did
Full name 3-Dimensional Interacting Domains
Description The database of three-dimensional interacting domains (3did) is a collection of high-resolution three-dimensional structural templates for domain-domain interactions.
URL http://3did.irbbarcelona.org/
Year founded 2005
Last update & version 3/27/2014    v1.0
Availability Free to all users
University/Institution hosted Institute for Research in Biomedicine
Address c/ Baldiri Reixac 10-12,08028 Barcelona,Spain
City Barcelona
Province/State
Country/Region Spain
Contact name Patrick Aloy
Contact email patrick.aloy@irbbarcelona.org
Data type(s)
Major organism(s)
Keyword(s)
  • domain-domain interaction
Publication(s)
  • 3did: a catalog of domain-based interactions of known three-dimensional structure. [PMID: 24081580]

    Roberto Mosca, Arnaud Céol, Amelie Stein, Roger Olivella, Patrick Aloy
    Nucleic acids research 2014:42(Database issue)
    45 Citations (Google Scholar as of 2016-05-29)

    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.

  • 3did: identification and classification of domain-based interactions of known three-dimensional structure. [PMID: 20965963]

    Amelie Stein, Arnaud Céol, Patrick Aloy
    Nucleic acids research 2011:39(Database issue)
    109 Citations (Google Scholar as of 2016-01-20)

    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.

  • 3did Update: domain-domain and peptide-mediated interactions of known 3D structure. [PMID: 18953040]

    Amelie Stein, Alejandro Panjkovich, Patrick Aloy
    Nucleic acids research 2009:37(Database issue)
    63 Citations (Google Scholar as of 2016-01-20)

    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.

  • 3did: interacting protein domains of known three-dimensional structure. [PMID: 15608228]

    Amelie Stein, Robert B Russell, Patrick Aloy
    Nucleic acids research 2005:33(Database issue)
    182 Citations (Google Scholar as of 2016-01-20)

    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.

Community reviews

Data
quality & quantity
Content organization & presentation
System accessibility & reliability
Reviewed by

Word cloud (embeddable)

Database Commons - Word Cloud

Accessibility

Rate of accessibility:
HTTP status codeDate requested
-1 Failed2018-11-16
-1 Failed2018-11-13
-1 Failed2018-11-09
-1 Failed2018-11-06
-1 Failed2018-11-02
-1 Failed2018-10-30
-1 Failed2018-10-26
-1 Failed2018-10-23
-1 Failed2018-10-19
-1 Failed2018-10-16
-1 Failed2018-10-12
-1 Failed2018-10-09
-1 Failed2018-10-05
-1 Failed2018-10-02
-1 Failed2018-09-28
-1 Failed2018-09-25
-1 Failed2018-09-21
-1 Failed2018-09-18
-1 Failed2018-09-14
-1 Failed2018-09-11
-1 Failed2018-09-07
-1 Failed2018-09-04
-1 Failed2018-08-31
-1 Failed2018-08-28
-1 Failed2018-08-24
-1 Failed2018-08-21
-1 Failed2018-08-17
-1 Failed2018-08-14
-1 Failed2018-08-10
-1 Failed2018-08-07
-1 Failed2018-08-03
-1 Failed2018-07-31
-1 Failed2018-07-27
-1 Failed2018-07-24
-1 Failed2018-07-20
-1 Failed2018-07-17
-1 Failed2018-07-13
-1 Failed2018-07-10
-1 Failed2018-07-06
-1 Failed2018-07-03
-1 Failed2018-06-29
-1 Failed2018-06-26
-1 Failed2018-06-22
-1 Failed2018-06-19
-1 Failed2018-06-15
-1 Failed2018-06-12
-1 Failed2018-06-08
-1 Failed2018-06-05
-1 Failed2018-06-01
-1 Failed2018-05-29
-1 Failed2018-05-25
-1 Failed2018-05-22
-1 Failed2018-05-18
-1 Failed2018-05-15
-1 Failed2018-05-11
-1 Failed2018-05-08
-1 Failed2018-05-04
-1 Failed2018-05-01
-1 Failed2018-04-27
-1 Failed2018-04-24
-1 Failed2018-04-20
-1 Failed2018-04-17
-1 Failed2018-04-13
-1 Failed2018-04-10
-1 Failed2018-04-06
-1 Failed2018-04-03
-1 Failed2018-02-27
-1 Failed2018-02-23
-1 Failed2018-02-20
-1 Failed2018-02-16
-1 Failed2018-02-13
-1 Failed2018-02-09
-1 Failed2018-02-06
-1 Failed2018-02-02
-1 Failed2018-01-30
-1 Failed2018-01-26
-1 Failed2018-01-23
-1 Failed2018-01-19
-1 Failed2018-01-16
-1 Failed2018-01-12
-1 Failed2018-01-09
-1 Failed2018-01-05
-1 Failed2018-01-02
-1 Failed2017-12-29
-1 Failed2017-12-26
-1 Failed2017-12-22
-1 Failed2017-12-19
-1 Failed2017-12-15
-1 Failed2017-12-12
-1 Failed2017-12-08
-1 Failed2017-12-05
-1 Failed2017-12-01
-1 Failed2017-11-28
-1 Failed2017-11-24
-1 Failed2017-11-21
-1 Failed2017-11-17
-1 Failed2017-11-14
-1 Failed2017-11-10
-1 Failed2017-11-07
-1 Failed2017-11-03
-1 Failed2017-10-31
-1 Failed2017-10-27
-1 Failed2017-10-24
-1 Failed2017-10-20
-1 Failed2017-10-17
-1 Failed2017-10-13
-1 Failed2017-10-10
-1 Failed2017-10-06
-1 Failed2017-10-03
-1 Failed2017-09-29
200 OK2017-09-26
200 OK2017-09-22
200 OK2017-09-19
200 OK2017-09-15
200 OK2017-09-12
200 OK2017-09-08
200 OK2017-09-05
200 OK2017-09-01
200 OK2017-08-29
200 OK2017-08-25
200 OK2017-08-22
200 OK2017-08-18
200 OK2017-08-15
200 OK2017-08-11
200 OK2017-08-08
200 OK2017-08-04
200 OK2017-08-01
200 OK2017-07-28
200 OK2017-07-25
200 OK2017-07-21
200 OK2017-07-18
200 OK2017-07-14
200 OK2017-07-04
200 OK2017-06-30
200 OK2017-06-27
200 OK2017-06-23
200 OK2017-06-20
200 OK2017-06-16
200 OK2017-06-13
200 OK2017-06-09
200 OK2017-06-06
200 OK2017-06-02
200 OK2017-05-30
200 OK2017-05-26
200 OK2017-05-23
200 OK2017-05-19
200 OK2017-05-16
200 OK2017-05-12
200 OK2017-05-09
200 OK2017-05-05
200 OK2017-05-02
200 OK2017-04-28
200 OK2017-04-25
200 OK2017-04-21
200 OK2017-04-18
200 OK2017-04-14
200 OK2017-04-11
200 OK2017-04-07
200 OK2017-04-04
200 OK2017-03-31
200 OK2017-03-28
200 OK2017-03-24
200 OK2017-03-21
200 OK2017-03-17
200 OK2017-03-14
200 OK2017-03-10
200 OK2017-03-07
200 OK2017-03-03
200 OK2017-02-28
200 OK2017-02-24
200 OK2017-02-21
200 OK2017-02-17
200 OK2017-02-14
200 OK2017-02-10
200 OK2017-02-07
200 OK2017-02-03
200 OK2017-01-31
200 OK2017-01-27
200 OK2017-01-24
200 OK2017-01-20
200 OK2017-01-17
200 OK2017-01-13
200 OK2017-01-10
200 OK2017-01-06
200 OK2017-01-03
200 OK2016-12-30
200 OK2016-12-27
200 OK2016-12-23
200 OK2016-12-20
200 OK2016-12-16
200 OK2016-12-13
200 OK2016-12-09
200 OK2016-12-06
200 OK2016-12-02
200 OK2016-11-29
200 OK2016-11-25
200 OK2016-11-22
200 OK2016-11-18
200 OK2016-11-15
200 OK2016-11-11
200 OK2016-11-08
200 OK2016-11-04
-1 Failed2016-11-01
-1 Failed2016-10-28
200 OK2016-10-25
200 OK2016-10-21
200 OK2016-10-18
200 OK2016-10-14
200 OK2016-10-11
200 OK2016-10-07
200 OK2016-10-04
200 OK2016-09-30
200 OK2016-09-27
200 OK2016-09-23
200 OK2016-09-20
200 OK2016-09-16
200 OK2016-09-13
200 OK2016-09-09
200 OK2016-09-06
200 OK2016-09-02
200 OK2016-08-30
200 OK2016-08-26
200 OK2016-08-23
200 OK2016-08-19
200 OK2016-08-16
200 OK2016-08-12
200 OK2016-08-09
200 OK2016-08-05
200 OK2016-08-02
200 OK2016-07-29
200 OK2016-07-26
200 OK2016-07-22
200 OK2016-07-19
200 OK2016-07-15
200 OK2016-07-12
200 OK2016-07-08
200 OK2016-07-05
200 OK2016-07-01
200 OK2016-06-28
200 OK2016-06-24
200 OK2016-06-21
200 OK2016-06-17
200 OK2016-06-14
200 OK2016-06-10
200 OK2016-06-07
200 OK2016-06-03
200 OK2016-05-31
200 OK2016-05-27
200 OK2016-05-24
200 OK2016-05-20
200 OK2016-05-17
200 OK2016-05-13
200 OK2016-05-10
200 OK2016-05-06
200 OK2016-05-03
200 OK2016-04-29
200 OK2016-04-26
200 OK2016-04-22
200 OK2016-04-19
200 OK2016-04-15
200 OK2016-04-12
200 OK2016-04-08
200 OK2016-04-05
200 OK2016-04-01
200 OK2016-03-29
200 OK2016-03-28
200 OK2016-03-25
200 OK2016-03-23
200 OK2016-03-21
200 OK2016-03-18
200 OK2016-03-16
200 OK2016-03-14
200 OK2016-03-11
200 OK2016-03-09
200 OK2016-03-07
200 OK2016-03-04
200 OK2016-03-02
200 OK2016-02-29
200 OK2016-02-26
200 OK2016-02-24
200 OK2016-02-22
200 OK2016-02-19
200 OK2016-02-17
200 OK2016-02-15
200 OK2016-02-14
200 OK2016-02-12
200 OK2016-02-10
200 OK2016-02-08
200 OK2016-02-07
200 OK2016-02-05
200 OK2016-02-03
200 OK2016-02-01
200 OK2016-01-31
200 OK2016-01-29
200 OK2016-01-27
200 OK2016-01-25
200 OK2016-01-24
200 OK2016-01-22
200 OK2016-01-20
200 OK2016-01-18
200 OK2016-01-17
200 OK2016-01-15
200 OK2016-01-13
200 OK2016-01-11
200 OK2016-01-10
200 OK2016-01-08
200 OK2016-01-06
200 OK2016-01-04

Tags

Interaction and Network Protein Structure
domain-domain interaction

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Zhang Zhang [2016-05-29]
    • Mengwei Li [2016-03-31]
    • Mengwei Li [2016-02-18]
    • Lina Ma [2015-11-24]
    • Mengwei Li [2015-11-21]
    • Lina Ma [2015-06-30]
    • Mengwei Li [2015-06-29]
    • Mengwei Li [2015-06-26]
Stats