Open position for Junior Researcher
Interactomics
List-of-links for existing online resources (DB, software, methods).
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(Agile Protein Interaction DataAnalyzer) is an interactive bioinformatic web-tool that has been developed to allow exploration and analysis of main currently known information about protein-protein interactions integrated and unified in a common and comparative platform. The analytical and integrative effort done in APID provides an open access frame where all known experimentally validated protein-protein interactions are unified in a unique web application that allows an agile exploration of the interactome network and includes certain calculated parameters that weight the reliability of a given interaction (i.e. the "edges" of the interactome network) between two proteins, and also qualify the functional environment around any given protein (i.e. the "nodes" of the interactome network) . |
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Biomolecular INteraction Network Database at the University of Toronto, Canada. No species restriction |
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PPI section of the Comprehensive Yeast Genome Database. Manually curated comprehensive S. cerevisiae PPI database at MIPS |
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Database of Interacting Proteins at UCLA. No species
restriction. Experimentally determined interactions between proteins. Combined information from variety of sources to create a single, consistent set of protein-protein interactions. |
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General Repository for Interaction Datasets. Mount Sinai Hospital, Toronto, Canada |
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Interactions between HIV and host proteins. |
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The Human Protein Reference Database. Institute of Bioinformatics, Bangalore, India and Johns Hopkins University, Baltimore, MD, USA. |
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Human Protein Interaction Database. Department of computer Science and Information Engineering Inha University, Inchon, Korea |
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iHOP (Information Hyperlinked over Proteins). Protein association network built by literature mining |
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Protein interaction database at EBI. No species restriction. Check also this node http://cbi.labri.fr/eng/intact.htm The Intact project, lead by EBI within the european TEMBLOR (The European Molecular Biology Linked Original resources) framework aims at developing a european federative database of protein-protein interactions and their annotations. |
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Database of putative interacting protein domains. Institute for InfoComm Research, Singapore. |
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PPI site at the Jena Centre for Bioinformatics, Germany |
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Commercial software suite and database. Manually curated human PPIs (among other things). GeneGo |
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Molecular INTeraction database at the Centro di Bioinformatica Molecolare, Universita di Roma, Italy. An inferred human network: HOMOMINT |
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| Mammalian protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. The included data refer to individually performed experiments providing the most reliable evidence for physical interactions. |
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Commented list of links to PPI databases and resources maintained at the MRC Rosalind Franklin Cetre for Genomics Research, Cambridge, UK |
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The Online Predicted Human Interaction Database. Ontario Cancer Institute and University of Toronto, Canada. |
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Information on protein-interaction domains. |
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Database of PDZ mediated protein-protein interactions. |
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Predicted functional associations and interactions. Boston University. |
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Analysis of protein-protein interfaces of protein complexes from PDB. University College of London, UK. |
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Proteomics and PPI tool/database. CuraGen Corporation. |
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Hybrigenics PPI data and tool, H. pylori. Free academic license available |
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Experimental and literature PPIs in mouse. |
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Protein networks based on experimental data and predictions at EMBL. |
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"BioKnowledge Library" at Incyte Corporation. Manually curated PPI data from S. cerevisiae. Proprietary. |
PPI related software
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Commercial graph layout software |
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Open source software for visualization of PPI networks and data integration |
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Graph layout software |
Other tools
Protein-protein interaction graphs visualisation tool.
Analysis and Visualization of Large Networks.The PRIMOS (Protein Interaction and Molecule Search) database operates as an integrated knowledge portal for analysing integrated protein-protein interaction data.
Besides standard search options like public identifier searches, our advanced searches provide the possibility of analysing protein-protein interaction datasets integrated from multiple datasources.
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Network Hub Search: Highly connected protein interaction nodes are likely to represent cores of molecular networks. This search option allows to search for such protein hubs with a minimum number of public protein-protein interaction in a given organism
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Organism Cross-Talk Interaction Search: The identification of cross-talk interaction between organisms is of particular importance for the investigation of pathogen and host protein-protein interactions. This search option allows to search for protein-protein interactions between two organisms and the option of specifying a certain experimental method that revealed this interaction.
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Confirmed Interaction Search: For the identification of trustable, meaning protein-protein interactions confirmed by multiple experimental methods this search option can be used.
Based on these principles, the system allows to submit a list of sequence identifiers in order to retrieve similar sets. It also allows to compare all the sets of a collection (hierarchical clustering of expression profiles for example) to all the sets of one or more other collections (KEGG pathways, GeneOntology and EC numbers for example). This feature allows the rapid identification of biological functions of co-expressed clusters of genes as well as the identification of genome wide features relationships such as the relation between the co-localization of genes on chromosomes (operons) and the protein interactions or the co-intervention in biological pathways.