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IntAct: an open source molecular interaction database

H. Hermjakob
2004 Nucleic Acids Research  
IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions.  ...  All IntAct software, data and controlled vocabularies are available at http://www.ebi.ac.uk/intact.  ...  IntAct provides a comprehensive, open source database and analysis system for protein interactions which can be locally installed and adapted to the needs of the local organization, thereby reducing development  ... 
doi:10.1093/nar/gkh052 pmid:14681455 pmcid:PMC308786 fatcat:w2yaa3blanhh7ffh63qbungt5y

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.  ...  Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at  ...  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

The IntAct molecular interaction database in 2010

B. Aranda, P. Achuthan, Y. Alam-Faruque, I. Armean, A. Bridge, C. Derow, M. Feuermann, A. T. Ghanbarian, S. Kerrien, J. Khadake, J. Kerssemakers, C. Leroy (+9 others)
2009 Nucleic Acids Research  
IntAct is an open-source, open data molecular interaction database and toolkit.  ...  Specialized views then allows 'zooming in' on the full annotation of interactions, interactors and their properties. IntAct source code and data are freely available at  ...  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/gkp878 pmid:19850723 pmcid:PMC2808934 fatcat:rvotbwzdvnbxlctix6wui6znii

IntAct--open source resource for molecular interaction data

S. Kerrien, Y. Alam-Faruque, B. Aranda, I. Bancarz, A. Bridge, C. Derow, E. Dimmer, M. Feuermann, A. Friedrichsen, R. Huntley, C. Kohler, J. Khadake (+12 others)
2007 Nucleic Acids Research  
IntAct is an open source database and software suite for modeling, storing and analyzing molecular interaction data.  ...  IntAct supports and encourages local installations as well as direct data submission and curation collaborations. IntAct source code and data are freely available from http://www.ebi.ac.uk/intact.  ...  Funding to pay the Open Access publication charges for this article was provided by Felics. Conflict of interest statement. There are no conflict of interest.  ... 
doi:10.1093/nar/gkl958 pmid:17145710 pmcid:PMC1751531 fatcat:nuzqfjvlwvdq3dwcdvs3nxicei

The Relationship between the UniProt Knowledgebase (UniProtKB) and the IntAct Molecular Interaction Databases

Yasmin Alam-Faruque
2009 Nature Precedings  
European Bioinformatics Institute References: Features within a UniProtKB/SwissProt entry leading to connection with the IntAct database:  ...  IntAct is funded by the European Commission under FELICS, contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme.  ...  Statistics: Release 57.0 (of 24-Mar-09) of UniProtKB/Swiss-Prot contains 428650 sequence entries.IntAct provides a freely available, open source database system and analysis tools for protein-protein interaction  ... 
doi:10.1038/npre.2009.3936.1 fatcat:tokgm2ax4ng7nboy6o756bg5ju

The Relationship between the UniProt Knowledgebase (UniProtKB) and the IntAct Molecular Interaction Databases

Yasmin Alam-Faruque, Yasmin Alam-Faruque
2009 Nature Precedings  
European Bioinformatics Institute References: Features within a UniProtKB/SwissProt entry leading to connection with the IntAct database:  ...  IntAct is funded by the European Commission under FELICS, contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme.  ...  Statistics: Release 57.0 (of 24-Mar-09) of UniProtKB/Swiss-Prot contains 428650 sequence entries.IntAct provides a freely available, open source database system and analysis tools for protein-protein interaction  ... 
doi:10.1038/npre.2009.3936 fatcat:ubn53pnwvfgijeyw4wdklqenx4

IntAct App: a Cytoscape application for molecular interaction network visualisation and analysis

Eliot Ragueneau, Anjali Shrivastava, John H Morris, Noemi Del-Toro, Henning Hermjakob, Pablo Porras
2021 Bioinformatics  
IntAct App is a Cytoscape 3 application that grants in-depth access to IntAct's molecular interaction data.  ...  Implementation available at https://apps.cytoscape.org/apps/intactapp, while the source code is available at https://github.com/EBI-IntAct/IntactApp.  ...  Introduction IntAct is an open-source molecular interaction database which captures experimental evidence from the literature in high detail (Orchard et al., 2014) , following the deep curation model  ... 
doi:10.1093/bioinformatics/btab319 pmid:33961020 pmcid:PMC8545338 fatcat:owd2ky2yxnekzb7y35juh7u24q

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.  ...  Part of the motivation for providing the entire IntAct code base as open source was to reduce redundant development of interaction database platforms.  ... 
doi:10.1093/nar/gkt1115 pmid:24234451 pmcid:PMC3965093 fatcat:5qemzevwgzdjln3y4pxvgfz7aa

VisioProt-MS: interactive 2D maps from intact protein mass spectrometry

Marie Locard-Paulet, Julien Parra, Renaud Albigot, Emmanuelle Mouton-Barbosa, Laurent Bardi, Odile Burlet-Schiltz, Julien Marcoux, Alfonso Valencia
2018 Bioinformatics  
To our knowledge, this is the only open source standalone application that allows the dynamic comparison of several MS files, a prerequisite for comparative analysis of different biological conditions.  ...  VisioProt-MS is designed to summarize and analyze intact protein and top-down proteomics data.  ...  VisioProt-MS is a user-friendly and highly compatible open source web application that plots and overlays interactive 2 D maps from deconvoluted LC-MS run(s).  ... 
doi:10.1093/bioinformatics/bty680 pmid:30084957 fatcat:ouwswu6nyjakrlzmciukl332g4

Investigating Viral Proteins and Intact Viruses with Mass Spectrometry [chapter]

Sunia A. Trauger, Teri Junker, Gary Siuzdak
2003 Topics in current chemistry  
Mass spectrometry has become a fundamental technology for virology and an important tool in probing the structure and function of viruses.  ...  More recently, new mass spectrometry approaches have been used to detect intact viruses.  ...  These identifications were made using the molecular weight range of 0-100 kDa and the database searches were constrained to mammals for BSA and viruses for HK97.  ... 
doi:10.1007/3-540-36113-8_8 fatcat:3r2f4fwmarashhralqdwsnzkz4

Dual Role of Functionally Intact Dyadic Junctions in Cardiac Excitation-Contraction Coupling

Prakash Subramanyam, Donald D. Chang, Henry M. Colecraft
2015 Biophysical Journal  
Altogether, the results shed new light on molecular determinants important for CaV1.2 functional targeting in cardiomyocytes, and suggest a new unconventional role for functionally intact dyads-as being  ...  Since cAMP activates the kinase PKA, which in turn increases Ca 2þ release through sarcoplasmic reticulum RyR channels, CaSF was measured as an index of RyR open probability.  ... 
doi:10.1016/j.bpj.2014.11.1467 fatcat:khd5roo35zagjf6jy6ruc3cr4a

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Caroline Haupt, Tommy Hofmann, Sabine Wittig, Susann Kostmann, Argyris Politis, Carla Schmidt
2017 Journal of Visualized Experiments  
Mass spectrometry of intact protein complexes (sometimes called 'native' mass spectrometry), on the other hand, involves the analysis of intact proteins and protein complexes without hydrolysis into peptides  ...  It reveals protein stoichiometries as well as protein and ligand interactions.  ...  The results from BS3 cross-linking are visualized in an interaction network ( Figure 3D) showing intra-molecular interactions as well as interactions between different subunits.  ... 
doi:10.3791/56747 pmid:29286378 pmcid:PMC5755487 fatcat:wg2vkc5gy5ecbia2elye3oozm4

Large-scale intact glycopeptide identification by Mascot database search

Ravi Chand Bollineni, Christian Jeffrey Koehler, Randi Elin Gislefoss, Jan Haug Anonsen, Bernd Thiede
2018 Scientific Reports  
We present an approach for automated annotation of intact glycopeptide mass spectra.  ...  glycoprotein databases.  ...  against protein databases to generate molecular networks for intact large scale glycopeptide identification.  ... 
doi:10.1038/s41598-018-20331-2 pmid:29391424 pmcid:PMC5795011 fatcat:cx5d5iq45jfg3l2kcqbrog2g4e

Different Stationary Phase Selectivities and Morphologies for Intact Protein Separations

A. Astefanei, I. Dapic, M. Camenzuli
2016 Chromatographia  
, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution  ...  In order to achieve efficiencies comparable to those of good packed columns, porous layer open tubular (PLOT) columns must have an inner diameter of the order of 15 μm or less.  ... 
doi:10.1007/s10337-016-3168-z pmid:28529348 pmcid:PMC5413533 fatcat:yqnb7cr52bdafhelms6ou4g2ym

The indoor environment - a potent source for intact human-associated anaerobes [article]

Manuela Raluca Pausan, Marcus Blohs, Alexander Mahnert, Christine Moissl-Eichinger
2020 bioRxiv   pre-print
Less than 25% of the prokaryotic signatures originate from intact - and thus potentially living - cells with an apparent survival advantage for aerobic and stress resistant taxa.  ...  As interaction and exchange of microbes between the human body and its environment is crucial for a healthy human microbiome, the built environment (BE) might represent a potent source for commensal microbes  ...  Whether obligately anaerobic human commensals can be transmitted between individuals via the BE is still an open question.  ... 
doi:10.1101/2020.12.02.406132 fatcat:e3nbrece4rcefmbjintpyjetya
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