max planck institut
informatik
informatik
This page is devoted to the data sources that form the foundation of DASMIweb.
DASMIweb currently has access to 35 distributed data sources. 9 of these provide interaction data that has been experimentally determined or curated from the scientific literature, 24 data sources contain computational predictions, and 2 data sources can be used for scoring the quality of interactions.
Though it contradicts the decentralization principles of DASMI and DASMIweb, we temporarily cache 28 external datasets at our institute to make them available via DASMIweb. In the table below, you can identify these datasets by their 'Other details' tags.
Should you wish to download one of the temporarily cached datasets for offline analysis, please visit our download page. However, note that we will remove temporary caches and download options as soon as the original data providers render these unneccesssary by setting up respective data servers.
Importantly, we would like to cordially thank all providers of interaction data or interacion confidence scores that support the distributed system by setting up servers for their data.
If you feel that you resource should also be mentioned here, or that your resource should not be mentioned here (i.e. should not be accessible via DASMIweb), please contact us
| Name | Link to resource | Publication / description | Data determination method | Other details |
|---|---|---|---|---|
| MPIDB | http://www.jcvi.org/mpidb/about.php | Goll et al. (2008). MPIDB: the microbial protein interaction database. Bioinformatics, 24(15):1743-1744; | literature curated | |
| IntAct | http://www.ebi.ac.uk/intact/site/index.jsf | Kerrien et al. (2007). IntAct-open source resource for molecular interaction data. Nucleic Acids Res, 35(Database issue):D561-D565. | literature curated | |
| 3did | http://gatealoy.pcb.ub.es/3did/ | Stein et al. (2008). 3did Update: domain-domain and peptide-mediated interactions of known 3D structure. Nucleic Acids Res, 37(Database issue):D300-D304. | crystal structure analysis | temporarily cached version: update, 2008-10-15 |
| APMM1 | http://intelligent.eic.osaka-sandai.ac.jp/chenen/MDCinfer.htm | Wang et al. (2007). Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformactics, 8(1):391 | predicted | final dataset |
| APMM2 | http://intelligent.eic.osaka-sandai.ac.jp/chenen/MDCinfer.htm | Wang et al. (2007). Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformactics, 8(1):391 | predicted | final dataset |
| Bioverse | http://bioverse.compbio.washington.edu/ | McDermott et al. (2005). Functional annotation from predicted protein interaction networks. Bioinformatics, 21(15):3217-3226. | predicted | final dataset |
| CCSB-HI1 | http://vidal.dfci.harvard.edu/ | Rual et al. (2005). Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437(7062):1173-1178. | experimental | final dataset |
| DIMA-DPEA | http://mips.gsf.de/genre/proj/dima2/ | Pagel et al. (2008). DIMA 2.0-predicted and known domain interactions. Nucleic Acids Res, 36, D651-D655. | predicted | temporarily cached version: 2.0, 2007-11-13 |
| DIMA-DPROF | http://mips.gsf.de/genre/proj/dima2/ | Pagel et al. (2008). DIMA 2.0-predicted and known domain interactions. Nucleic Acids Res, 36, D651-D655. | predicted | temporarily cached version: 2.0, 2007-11-13 |
| DIMA-STRING | http://mips.gsf.de/genre/proj/dima2/ | Pagel et al. (2008). DIMA 2.0-predicted and known domain interactions. Nucleic Acids Res, 36, D651-D655. | predicted | temporarily cached version: 2.0, 2007-11-13 |
| DIP | http://dip.doe-mbi.ucla.edu/ | Salwinski et al. (2004). The Database of Interacting Proteins: 2004 update. Nucleic Acids Res, 32:D449-D451 | literature curated | temporarily cached version: 2009-01-26 |
| Domain support | http://www.dasmi.de | interaction quality measure | ||
| DPEA | http://genomebiology.com/2005/6/10/R89 | Riley et al. (2005). Inferring protein domain interactions from databases of interacting proteins. Genome Biol, 6(10):R89. | predicted | final dataset |
| FunSimMat2.1 | http://funsimmat.bioinf.mpi-inf.mpg.de/ | Schlicker and Albrecht. (2008). FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res, 36, D434-D439. | interaction quality measure | |
| HiMAP | http://www.himap.org/ | Rhodes et al. (2005). Probabilistic model of the human protein-protein interaction network. Nat Biotechnol, 23(8):951-959. | predicted | temporarily cached version: 2006-12-19 |
| HiMAP-core | http://www.himap.org/ | Rhodes et al. (2005). Probabilistic model of the human protein-protein interaction network. Nat Biotechnol, 23(8):951-959. | predicted | temporarily cached version: 2006-12-19 |
| HomoMINT | http://mint.bio.uniroma2.it/HomoMINT/Welcome.do | Persico et al. (2005). HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics, 6 Suppl 4:S21. | predicted | temporarily cached version: 2009-03-05 |
| HPRD | http://www.hprd.org | Keshava Prasad et al. (2009). Human Protein Reference Database-2009 update. Nucleic Acids Res, 37(Database issue):D767-D772 | literature curated | temporarily cached 2009-06-07 |
| InterDom | http://interdom.i2r.a-star.edu.sg/ | Ng et al. (2003). Integrative approach for computationally inferring protein domain interactions. Bioinformatics, 19(8):923-929. | predicted | temporarily cached version: v2, 2007-07-31 |
| iPfam | http://ipfam.sanger.ac.uk/ | Finn et al. (2005). iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions. Bioinformatics, 21(3):410-412. | crystal structure analysis | |
| IPPRI-HC | http://bioinformatics.oxfordjournals.org/cgi/content/full/24/16/i35 | High confidence subset of Schelhorn et al. (2008). An integrative approach for predicting interactions of protein regions. Bioinformatics, 24(16):i35-i41. | predicted | |
| IPPRI | http://bioinformatics.oxfordjournals.org/cgi/content/full/24/16/i35 | Schelhorn et al. (2008). An integrative approach for predicting interactions of protein regions. Bioinformatics, 24(16):i35-i41. | predicted | |
| LDSC | http://www.biomedcentral.com/1471-2105/7/269 | Lee et al. (2006). An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics, 7:269. | predicted | final dataset |
| LDSC-core | http://www.biomedcentral.com/1471-2105/7/269 | Lee et al. (2006). An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics, 7:269. | predicted | final dataset |
| LLZ | http://bioinformatics.med.yale.edu/interaction/ | Liu et al. (2005). Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics, 21(15):3279-3285. | predicted | final dataset |
| LP | http://genomebiology.com/2006/7/11/R104 | Guimaraes. et al. (2006). Predicting domain-domain interactions using a parsimony approach. Genome Biol, 7(11):R104. | predicted | final dataset |
| MDC | http://www.ncbi.nlm.nih.gov/pubmed/16169070 | Stelzl et al. (2005). A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122(6):957-968. | experimental | final dataset |
| OPHID | http://ophid.utoronto.ca/ophid/ | Brown and Jurisica (2005). Online predicted human interaction database. Bioinformatics, 21(9):2076-2082. | predicted | temporarily cached version: 2009-08-03 |
| PInS | http://pins.ornl.gov/ | Bordner and Gorin (2008). Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. BMC Bioinformatics, 9:234. | crystal structure analysis | final dataset |
| POINT | http://insilico.csie.ntu.edu.tw:9999/point/ | Huang et al. (2004). POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome. Bioinformatics, 20(17):3273-3276. | predicted | final dataset |
| RCDP50 | http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1618801 | Jothi et al. (2006). Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol, 362(4):861-75. | predicted | final dataset |
| RDFF | http://www.ittc.ku.edu/~xwchen/PPI/random_forest_PPI | Chen et al. (2005). Prediction of protein-protein interactions using random decision forest framework. Bioinformatics, 21(24):4394-400. | predicted | final dataset |
| Sanger | http://genomebiology.com/2004/5/9/R63 | Lehner and Fraser (2004). A first-draft human protein interaction map. Genome Biol, 5(9):R63. | predicted | final dataset |
| Sanger-core | http://genomebiology.com/2004/5/9/R63 | Lehner and Fraser (2004). A first-draft human protein interaction map. Genome Biol, 5(9):R63. | predicted | final dataset |
| TW | http://www.biomedcentral.com/1471-2164/7/122/abstract | Wuchty et al. (2006). Topology and weights in a protein domain interaction network-a novel way to predict protein interactions. BMC Genomcis, 7:122. | predicted | final dataset |