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The IntAct molecular interaction database in 2012

S. Kerrien, B. Aranda, L. Breuza, A. Bridge, F. Broackes-Carter, C. Chen, M. Duesbury, M. Dumousseau, M. Feuermann, U. Hinz, C. Jandrasits, R. C. Jimenez (+10 others)
2011 Nucleic Acids Research  
IntAct is an open-source, open data molecular interaction database and toolkit.  ...  In response to the growing data volume and user requests, IntAct now provides a two-tiered view of the interaction data.  ...  ACKNOWLEDGEMENTS The authors thank Paula de Matos and the EBI ChEBI team for the development of the chemical search module in IntAct.  ... 
doi:10.1093/nar/gkr1088 pmid:22121220 pmcid:PMC3245075 fatcat:5grh3dougnbuxkosirzc5wkizi

ComplexViewer: visualization of curated macromolecular complexes

Colin W Combe, Marine (Dumousseau) Sivade, Henning Hermjakob, Joshua Heimbach, Birgit H M Meldal, Gos Micklem, Sandra Orchard, Juri Rappsilber, Jonathan Wren
2017 Bioinformatics  
Furthermore, if binding regions between molecules are known then these can be displayed in the context of the larger complex.  ...  ComplexViewer visualizes interactions with more than two participants and thereby avoids the need to first expand these into multiple binary interactions.  ...  The IMEx Consortium (Orchard et al., 2012) is an international collaboration designed to systematically capture published interaction data in publicly available databases.  ... 
doi:10.1093/bioinformatics/btx497 pmid:29036573 pmcid:PMC5870653 fatcat:kpee5g2y4zcy5c5vpcjjuz6doq

The cardiovascular gene annotation initiative: current and future aims

R.C. Lovering, N.H. Campbell, A.N. Melidoni, M. Rodriguez-Lopez, R.P. Huntley, T. Sawford, C. O'Donovan, M. Martin, S. Orchard, H. Hermjakob, M. Mayr, R. Apweiler (+2 others)
2014 Atherosclerosis  
the GO and IntAct databases and provide key resources for researchers wishing to understand the biological role of a gene product. • We will be dividing our time equally between using Gene Ontology (GO  ...  GO contains three structured controlled vocabularies (ontologies) that describe gene products in terms of their associated biological processes, subcellular locations and molecular functions, in a species-independent  ...  . • The IntAct molecular interaction database in 2012. Kerrien S. et al. Nucleic Acids Res. 40, D841-846 (2012). PMID 22121220. • Progress in genetic association studies of plasma lipids.  ... 
doi:10.1016/j.atherosclerosis.2014.10.062 fatcat:6bi3nthgvzduvibqj5qurjgan4

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

Sandra Orchard, Samuel Kerrien, Sara Abbani, Bruno Aranda, Jignesh Bhate, Shelby Bidwell, Alan Bridge, Leonardo Briganti, Fiona S L Brinkman, Gianni Cesareni, Andrew Chatr-aryamontri, Emilie Chautard (+19 others)
2012 Nature Methods  
perspective nature methods | VOL.9 NO.4 | APRIL 2012 | 345 the international molecular exchange (imex) consortium is an international collaboration between major public interaction data providers to share  ...  This is not due to lack of resources in this domain. As of December 2011, the PathGuide resource 1 listed more than 100 protein-protein interaction-related databases.  ...  In 2002, several providers of proteininteraction data, among them Biomolecular Interaction Network database (BIND) 4 , Database of Interacting Proteins (DIP) 5 , Hybrigenics 6 , IntAct 7 , Molecular Interaction  ... 
doi:10.1038/nmeth.1931 pmid:22453911 pmcid:PMC3703241 fatcat:ev2rpzb3c5hkpo52af3rfglfou

The MIntAct project—IntAct as a common curation platform for 11 molecular interaction databases

Sandra Orchard, Mais Ammari, Bruno Aranda, Lionel Breuza, Leonardo Briganti, Fiona Broackes-Carter, Nancy H. Campbell, Gayatri Chavali, Carol Chen, Noemi del-Toro, Margaret Duesbury, Marine Dumousseau (+23 others)
2013 Nucleic Acids Research  
IntAct (freely available at http://www.ebi.ac.uk/ intact) is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions  ...  All data manually curated by the MINT curators have been moved into the IntAct database at EMBL-EBI and are merged with the existing IntAct dataset.  ...  The IntAct molecular interaction database has existed since 2002 to serve richly curated molecular interaction data provided in community accepted standard formats to a broad user community (2) .  ... 
doi:10.1093/nar/gkt1115 pmid:24234451 pmcid:PMC3965093 fatcat:5qemzevwgzdjln3y4pxvgfz7aa

Neighbor communities in drug combination networks characterize synergistic effect

Jun Zou, Pan Ji, Ying-Lan Zhao, Lin-Li Li, Yu-Quan Wei, Yu-Zong Chen, Sheng-Yong Yang
2012 Molecular Biosystems  
The target information of the 350 unique drugs was retrieved from database ChEMBL, TTD, and DrugBank.  ...  , HPRD, IntAct and MINT.  ...  Supplementary Material (ESI) for Molecular BioSystems This journal is © The Royal Society of Chemistry 2012 -ESI 11 -<File: Table_S10.xlsx>Table S10 The list of 445 adverse drug interactions.  ... 
doi:10.1039/c2mb25267h pmid:23014807 fatcat:6oa4oejgsraovcqof33hncaguq

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

Karin Breuer, Amir K. Foroushani, Matthew R. Laird, Carol Chen, Anastasia Sribnaia, Raymond Lo, Geoffrey L. Winsor, Robert E. W. Hancock, Fiona S. L. Brinkman, David J. Lynn
2012 Nucleic Acids Research  
In this article, we provide details of recent updates and improvements to the database.  ...  In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks,  ...  Thanks also to the various interaction, pathway and annotation databases that have been integrated into InnateDB for freely providing their data to the public.  ... 
doi:10.1093/nar/gks1147 pmid:23180781 pmcid:PMC3531080 fatcat:jmmbldnvuzgg7fm4vjbqnoknrm

PRD: A protein–RNA interaction database

Shigeo Fujimori, Katsuya Hino, Ayumu Saito, Satoru Miyano, Etsuko Miyamoto-Sato
2012 Bioinformation  
Database Volume 8(15) ISSN 0973-2063 (online) 0973-8894 (print) Bioinformation 8(15): 729-730 (2012) 729 Abstract: Although protein-RNA interactions (PRIs) are involved in various important cellular processes  ...  Users can browse all recorded interactions and execute flexible keyword searches against the database via a web interface.  ...  Koichi Takeda for their helpful comments on the database construction.  ... 
doi:10.6026/97320630008729 pmid:23055619 pmcid:PMC3449375 fatcat:xookxiz4qrcu5cp35o2tpvilim

The Intricacy of the Viral-Human Protein Interaction Networks: Resources, Data, and Analyses

Deeya Saha, Marta Iannuccelli, Christine Brun, Andreas Zanzoni, Luana Licata
2022 Frontiers in Microbiology  
Experimental protein-protein interactions described in the scientific literature have been systematically captured into several molecular interaction databases.  ...  Among them, the study of virus-host protein-protein interactions is a powerful strategy to comprehend the molecular mechanisms employed by the virus to infect the host cells and to interact with their  ...  AZ and LL wrote the first draft of the manuscript. DS, MI, and CB wrote sections of the manuscript. DS prepared the figure.  ... 
doi:10.3389/fmicb.2022.849781 pmid:35531299 pmcid:PMC9069133 fatcat:lpscrnk2azd2xkshvl6r2wyu7i

References [chapter]

2012 Data Management of Protein Interaction Networks  
Intact: an open source molecular interaction database . Nucleic Acids Res 1 ( 32 ): 452 -455 ( 2004 ). 20. K. R. Brown and I. Jurisica . Online predicted human interaction data- base .  ...  MIPS: a database for genomes and protein sequences . Gary Bader and Christopher Hogue . An automated method for fi nding molecular complexes in large protein interaction networks .  ... 
doi:10.1002/9781118103746.refs fatcat:ftc5jwenxjcbpjkqvqxgfb5jei

Reconstruction of the experimentally supported human protein interactome: what can we learn?

Maria I Klapa, Kalliopi Tsafou, Evangelos Theodoridis, Athanasios Tsakalidis, Nicholas K Moschonas
2013 BMC Systems Biology  
Understanding the topology and dynamics of the human protein-protein interaction (PPI) network will significantly contribute to biomedical research, therefore its systematic reconstruction is required.  ...  The latter are probably involved in specialized physiological conditions, justifying the scarcity of related PPI information, and their identification can assist in designing relevant functional experiments  ...  IntAct IntAct, a main partner of the International Molecular Exchange (IMEx) Consortium [10] , is a repository of molecular interaction data for multiple organisms [26] .  ... 
doi:10.1186/1752-0509-7-96 pmid:24088582 pmcid:PMC4015887 fatcat:dezkncgl3zaufonk67ff2dulri

Genomic and proteomic data integration for comprehensive biodata search

Arif Canakoglu, Marco Masseroli
2012 EMBnet journal  
Towards this aim, protein-protein interaction data files downloaded from MINT (Licata et al., 2012) and IntAct (Kerrien et al., 2012) databases were automatically parsed.  ...  With high-throughput technologies in the life sciences, particularly in molecular biology, the amount of data available has grown exponentially.  ... 
doi:10.14806/ej.18.b.561 fatcat:xsobecxiw5cxpf6z6e4uizbpoy

2PT107 A classification of enzymatic reactions and its application to metabolic pathway search(The 50th Annual Meeting of the Biophysical Society of Japan)
2PT107 酵素反応の分類と代謝パスウェイ検索への応用(日本生物物理学会第50回年会(2012年度))

Susumu Goto, Masaaki Kotera, Toshiaki Tokimatsu, Yuki Moriya, Zen-ichi Nakagawa, Ai Muto, Minoru Kanehisa
2012 Seibutsu Butsuri  
The INTACT database stored 70,OOO and 40.000 two-body protein-protein interaetions foT yeast and human, respectively.  ...  We used DIP, BOND, HPRD, IntAct and Mint databases for biochemica] interaetion data. We first evaluated the quality ofthe experimental data, and add the information a]ong with the interactien data.  ...  The INTACT database stored 70,OOO and 40.000 two-body protein-protein interaetions foT yeast and human, respectively.  ... 
doi:10.2142/biophys.52.s122_4 fatcat:ruvkrmfwvrb2nexjyow63a7lty

2PT104 Development of re-docking method by obtaining native interaction pattern(The 50th Annual Meeting of the Biophysical Society of Japan)
2PT104 相互作用プロファイルを使った正解相互作用部位の絞込みによる再ドッキング法の研究(日本生物物理学会第50回年会(2012年度))

Nobuyuki Uchikoga, Yuri Matsuzaki, Masahito Ohue, Yutaka Akiyama, Takatsugu Hirokawa
2012 Seibutsu Butsuri  
The INTACT database stored 70,OOO and 40.000 two-body protein-protein interaetions foT yeast and human, respectively.  ...  We used DIP, BOND, HPRD, IntAct and Mint databases for biochemica] interaetion data. We first evaluated the quality ofthe experimental data, and add the information a]ong with the interactien data.  ...  The INTACT database stored 70,OOO and 40.000 two-body protein-protein interaetions foT yeast and human, respectively.  ... 
doi:10.2142/biophys.52.s122_1 fatcat:qvxuegjy7zblxdfimh45vjb26u

2PT106 Integration of Structural and Biochemical Information into Protein Interaction Network(The 50th Annual Meeting of the Biophysical Society of Japan)
2PT106 分子ネットワークにおける構造情報と相互作用情報の統合(日本生物物理学会第50回年会(2012年度))

Yuji Kawakami, Akinori Sarai, Satoshi Fujii
2012 Seibutsu Butsuri  
The INTACT database stored 70,OOO and 40.000 two-body protein-protein interaetions foT yeast and human, respectively.  ...  We used DIP, BOND, HPRD, IntAct and Mint databases for biochemica] interaetion data. We first evaluated the quality ofthe experimental data, and add the information a]ong with the interactien data.  ...  The INTACT database stored 70,OOO and 40.000 two-body protein-protein interaetions foT yeast and human, respectively.  ... 
doi:10.2142/biophys.52.s122_3 fatcat:dthik2oqk5gr7pizs3rtfl7hxi
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