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MINT, the molecular interaction database: 2012 update

Luana Licata, Leonardo Briganti, Daniele Peluso, Livia Perfetto, Marta Iannuccelli, Eugenia Galeota, Francesca Sacco, Anita Palma, Aurelio Pio Nardozza, Elena Santonico, Luisa Castagnoli, Gianni Cesareni
2011 Nucleic Acids Research  
MINT has adopted the PSI-MI standards for the annotation and for the representation of molecular interactions and is a member of the IMEx consortium.  ...  MINT (http://mint.bio.uniroma2.it/mint) is a public repository for molecular interactions reported in peer-reviewed journals.  ...  MINT, the Molecular INTeraction database, participates in this community effort.  ... 
doi:10.1093/nar/gkr930 pmid:22096227 pmcid:PMC3244991 fatcat:73rcsyttxvbubdl436vmf2q4ma

Update of KDBI: Kinetic Data of Bio-molecular Interaction database

P. Kumar, B. C. Han, Z. Shi, J. Jia, Y. P. Wang, Y. T. Zhang, L. Liang, Q. F. Liu, Z. L. Ji, Y. Z. Chen
2009 Nucleic Acids Research  
Knowledge of the kinetics of biomolecular interactions is important for facilitating the study of cellular processes and underlying molecular events, and is essential for quantitative study and simulation  ...  Kinetic Data of Bio-molecular Interaction database (KDBI) has been developed to provide information about experimentally determined kinetic data of protein-protein, proteinnucleic acid, protein-ligand,  ...  To complement these databases for providing the kinetic data not yet covered by other databases, we have developed the Kinetic Data of Bio-molecular Interactions database [KDBI; (34) ] to provide experimentally  ... 
doi:10.1093/nar/gkn839 pmid:18971255 pmcid:PMC2686478 fatcat:t4jlakihprgtvihi4xgui7dgzm

VirusMINT: a viral protein interaction database

A. Chatr-aryamontri, A. Ceol, D. Peluso, A. Nardozza, S. Panni, F. Sacco, M. Tinti, A. Smolyar, L. Castagnoli, M. Vidal, M. E. Cusick, G. Cesareni
2009 Nucleic Acids Research  
The VirusMINT database (http://mint.bio.uniroma2. it/virusmint/) aims at collecting all protein interactions between viral and human proteins reported in the literature.  ...  Understanding the consequences on host physiology induced by viral infection requires complete understanding of the perturbations caused by virus proteins on the cellular protein interaction network.  ...  (b) The 'connect' button interrogates the MINT database for all interactions between the proteins displayed in the graph.  ... 
doi:10.1093/nar/gkn739 pmid:18974184 pmcid:PMC2686573 fatcat:5i3kju2xx5esnjonkbmzt5zoqe

MatrixDB, the extracellular matrix interaction database

E. Chautard, M. Fatoux-Ardore, L. Ballut, N. Thierry-Mieg, S. Ricard-Blum
2010 Nucleic Acids Research  
MatrixDB is a member of the International Molecular Exchange consortium (IMEx) and has adopted the PSI-MI standards for the curation and the exchange of interaction data.  ...  Only few databases report protein-polysaccharide interactions and, to the best of our knowledge, there is no other database of extracellular interactions.  ...  data format exchange and Sandra Orchard (EBI, Hinxton, UK) for guiding us through the curation process.  ... 
doi:10.1093/nar/gkq830 pmid:20852260 pmcid:PMC3013758 fatcat:uo2666qwfjcipjb6tixsfwhgrq

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.  ...  Interactions involving domains and/or residues of that protein sequence within an interaction database will then require a corresponding update to ensure the mapping to the updated sequence is correct.  ... 
doi:10.1093/nar/gkt1115 pmid:24234451 pmcid:PMC3965093 fatcat:5qemzevwgzdjln3y4pxvgfz7aa

GWIDD: Genome-wide protein docking database

Petras J. Kundrotas, Zhengwei Zhu, Ilya A. Vakser
2009 Nucleic Acids Research  
Structural information on interacting proteins is important for understanding life processes at the molecular level.  ...  Current database version (August 2009) contains 25 559 experimental and modeled 3D structures for 771 organisms spanned over the entire universe of life from viruses to humans.  ...  ACKNOWLEDGEMENTS Andrey Tovchigrechko and Tatiana Baronova made important contributions to GWIDD project at the earlier stages of development.  ... 
doi:10.1093/nar/gkp944 pmid:19900970 pmcid:PMC2808876 fatcat:a3wmlhagczhbvmfkt4xonvklsq

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.  ...  As of September 2009, IntAct contains over 200.000 curated binary interaction evidences.  ...  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

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.  ...  As of September 2009, IntAct contains over 200.000 curated binary interaction evidences.  ...  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

MatrixDB, a database focused on extracellular protein–protein and protein–carbohydrate interactions

Emilie Chautard, Lionel Ballut, Nicolas Thierry-Mieg, Sylvie Ricard-Blum
2009 Computer applications in the biosciences : CABIOS  
MatrixDB (http://matrixdb.ibcp.fr) is a database reporting mammalian protein-protein and protein-carbohydrate interactions involving extracellular molecules.  ...  It takes into account the full interaction repertoire of the extracellular matrix involving full-length molecules, fragments and multimers.  ...  Blanchet for his strong support in building the web site. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp025 pmid:19147664 pmcid:PMC2647840 fatcat:drk4tkxkfnav5pinjujfnisc74

ChemProt: a disease chemical biology database

O. Taboureau, S. K. Nielsen, K. Audouze, N. Weinhold, D. Edsgard, F. S. Roque, I. Kouskoumvekaki, A. Bora, R. Curpan, T. S. Jensen, S. Brunak, T. I. Oprea
2010 Nucleic Acids Research  
Here, we report ChemProt, a disease chemical biology database, which is based on a compilation of multiple chemical-protein annotation resources, as well as disease-associated proteinprotein interactions  ...  Results from the disease chemical biology database associate citalopram, an antidepressant, with osteogenesis imperfect and leukemia and bisphenol A, an endocrine disruptor, with certain types of cancer  ...  The current interactome contains 428 429 unique protein-proteins interactions derived from source databases such as BIND (34) , GRID (35) , MINT (36) , dip_full (37) , HPRD (38) , intact (39) , mppi  ... 
doi:10.1093/nar/gkq906 pmid:20935044 pmcid:PMC3013776 fatcat:onpzqrlqajdndlyaryk3ll7azq

iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence

B. Turner, S. Razick, A. L. Turinsky, J. Vlasblom, E. K. Crowdy, E. Cho, K. Morrison, I. M. Donaldson, S. J. Wodak
2010 Database: The Journal of Biological Databases and Curation  
Acknowledgements The authors wish to thank Sandra Orchard for helpful suggestions regarding several iRefWeb features. Conflict of interest statement. None declared. Author Contribution  ...  2010), MINT (11 November 2009), MPact (10 January 2008), MPPI (06 January 2004) and OPHID(18 July 2006).  ...  In contrast, MINT recorded a human interaction citing the same publication and shows no overlap with the other two databases.  ... 
doi:10.1093/database/baq023 pmid:20940177 pmcid:PMC2963317 fatcat:2o7m36ql4vdbbbix7venxl3i6m

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases

Tiago J. S. Lopes, Martin Schaefer, Jason Shoemaker, Yukiko Matsuoka, Jean−Fred Fontaine, Gabriele Neumann, Miguel A. Andrade-Navarro, Yoshihiro Kawaoka, Hiroaki Kitano
2011 Computer applications in the biosciences : CABIOS  
Results: We found that the evaluated databases are comparable in terms of node connectivity (i.e. proteins with few interaction partners also have few interaction partners in other databases), but may  ...  Here, we evaluated the characteristics of six interaction databases, incorporated tissue-specific gene expression information and finally, investigated if the most popular proteins of scientific literature  ...  ACKNOWLEDGEMENTS We are grateful to the skillful and critical reading of the manuscript by Amie Eisfeld-Fenney and fruitful discussions with Takeshi Hase. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btr414 pmid:21798963 fatcat:4bzihh5yi5e7rfmzwbornfamiy

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

Saikat Chowdhury, Ram Rup Sarkar
2015 Database: The Journal of Biological Databases and Curation  
solutions for future database development, which could be useful to the whole scientific community.  ...  This review not only helps to identify some novel and useful features, which are not yet included in any of the databases but also highlights their current limitations and subsequently propose the reasonable  ...  (A) NetPath, BioModels and Pathway Commons manually annotate each interaction of a pathway, whereas CPDB uses other PPI databases (e.g. MINT and BIOGRID) for the annotation of each reaction.  ... 
doi:10.1093/database/bau126 pmid:25632107 pmcid:PMC4309023 fatcat:b6y4vbdg7rfdrac5z3htaxdcji

How helpful are the protein-protein interaction databases and which ones? [article]

Akhilesh Kumar Bajpai, Sravanthi Davuluri, Kriti Tiwary, Sithalechumi Narayanan, Sailaja Oguru, Kavyashree Basavaraju, Deena Dayalan, Kavitha Thirumurugan, Kshitish K Acharya
2019 bioRxiv   pre-print
Protein-protein interactions (PPIs) are critical, and so are the databases and tools (resources) concerning PPIs.  ...  Overall, hPRINT, STRING and IID together retrieved ~94% of 'total' protein interactions available in the databases. The coverage of certain databases was skewed for some gene-types.  ...  Acknowledgements The authors thank colleagues at BdataA and Shodhaka Life Sciences Pvt. Ltd. for assistance in gathering some of the PPI data and analysis.  ... 
doi:10.1101/566372 fatcat:f46uga34djaarbpao2wgvzldu4

Human immunodeficiency virus type 1, human protein interaction database at NCBI

W. Fu, B. E. Sanders-Beer, K. S. Katz, D. R. Maglott, K. D. Pruitt, R. G. Ptak
2009 Nucleic Acids Research  
ACKNOWLEDGEMENTS We thank Dr Roger Miller and Dr Carl Dieffenbach, NIH/NIAID/DAIDS, for discussions and intellectual input throughout this project; Dr Mikhail Rozanov, NCBI, for support in updating the  ...  HIV-1 RefSeq record; Joel Gillman, NCBI, for providing database support; and Dr David Robertson and Dr John Pinney, University of Manchester, UK, for help with Figure 3 .  ...  In addition, to help facilitate the retrieval of related data, links to other database resources, such as the Database of Interacting Proteins (DIP; 3), the Molecular INTeraction Database (MINT; 4), the  ... 
doi:10.1093/nar/gkn708 pmid:18927109 pmcid:PMC2686594 fatcat:4jekuoasojffxagcxe4t7mhauu
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