Proteomics/Protein - Protein Interactions/Jena Links

Protein Interactions Jena Links Databases Cross-linking Page Edited and Updated by: Dan Surdyk E-mail: dfs6389@rit.edu This Section: __TOC__ Links from the Jena Center for Bioinformatics Page Please note that the following page of references was quoted from the following online source: http://www.imb-jena.de/jcb/ppi Experimental Data AllFuse (European Bioinformatics Institute) functional association of proteins in complete genomes http://cgg.ebi.ac.uk/services/allfuse/ ASEdb (Harvard University) Alanine Scanning Energetics DataBase database of hotspots in 3D protein structures http://thornlab.cgr.harvard.edu/hotspot/index.php Bacteriome.org (University of Toronto) bacterial protein interaction database database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase http://www.bacteriome.org/ BID (A & M University Texas) Binding Interface Database http://tsailab.org/BID/index.php BioGRID (Samuel Lunenfeld Research Institute) The General Repository for Interaction Datasets database of genetic and physical interactions http://www.thebiogrid.org/ BOND (Thomson Corp.) Biomolecular Object Network Databank new resource to perform cross-database searches of available sequence, interaction, complex and pathway information integrates a range of component databases including Genbank and BIND, the Biomolecular Interaction Network Database http://bond.unleashedinformatics.com/Action? (UCLA) Database of Interacting Proteins http://dip.doe-mbi.ucla.edu/DIP Drosophila Protein Interaction Map (PIM) Database (Wayne State University) http://proteome.wayne.edu/PIMdb.html EchoBASE (University of York) integrated post-genomic database for E. coli http://www.ecoli-york.org/ Genomic Knowledge Database (RIKEN, Institute of Physical and Chemical Research) integrates various types of biological and biomedical databases in order to discover disease-related cascades and medicinal target candidates http://fuminobmt.gsc.riken.jp/big/Research/Genomic%20Knowledge%20Base%20Research%20Team/ HIV-1 - Human Protein Interaction Database (NCBI) http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/index.html summary of all known interactions of HIV-1 proteins with host cell proteins, other HIV-1 proteins, or proteins from disease organisms associated with HIV / AIDS hp-DPI (National Health Research Institutes) Helicobacter Pylori Database of Protein Interactomes combined with experimental and inferring interactions http://dpi.nhri.org.tw/protein/hp/ORF/index.php HPID (Inha University) Human Protein Intercation Database http://wilab.inha.ac.kr/hpid/ HUGE ppi (Kazusa DNA Research Institute) database of protein-protein interactions between large KIAAproteins http://www.kazusa.or.jp/huge/ppi/ HUGE: Human Unidentified Gene-Encoded large proteins http://www.kazusa.or.jp/huge/ Human Protein Reference Database (Johns Hopkins University & The Institute of Bioinformatics, India) platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome http://www.hprd.org/ ICBS (University of California) Inter-Chain Beta-Sheets database http://contact14.ics.uci.edu/index.html KDBI (National University of Singapore) database of Kinetic Data of Bio-molecular Interactions http://xin.cz3.nus.edu.sg/group/kdbi/kdbi.asp KEGG BRITE (Kyoto University) Biomolecular Relations in Information Transmission and Expression functional hierarchies and binary relationships of biological entities http://www.genome.ad.jp/brite/brite.html MINT (CBM, Rome) Molecular INTeractions database database of functional interactions between biological molecules: RNA, DNA, proteins http://cbm.bio.uniroma2.it/mint/ DOMINO - DOMain peptide INteractiOns database, describing interactions mediated by protein-interaction domains http://mint.bio.uniroma2.it/domino/search/searchWelcome.do molmovdb.org (Yale University) database of macromolecular movements with associated tools for flexibility and geometric analysis http://molmovdb.mbb.yale.edu/ MPact (MIPS) yeast protein-protein interaction data contained in http://mips.gsf.de/genre/proj/mpact/index.html Comprehensive Yeast Genome Database http://mips.gsf.de/genre/proj/yeast/index.jspCYGD MPPI (MIPS) Mammalian Protein-Protein Interaction database http://mips.gsf.de/proj/ppi/ PDZBase (Weill Medical College of Cornell University) manually curated protein-protein interaction database developed specifically for interactions involving PDZ domains http://icb.med.cornell.edu/services/pdz/start PepCyber: P~PEP (University of Minnesota) database of human protein-protein interactions mediated by phosphoprotein binding domains (PPBDs) http://pepcyber.umn.edu/PPEP/ POINT (National Health Research Institutes & National Taiwan University) functional database for the prediction of the human protein-protein interactome based on available orthologous interactome datasets integrates several publicly accessible databases, with emphasis placed on the extraction of a large quantity of mouse, fruit fly, worm and yeast protein-protein interactions datasets from the Database of Interacting Proteins (DIP), followed by conversion of them into a predicted human interactome http://phos.bioinformatics.tw/ PRIME (Human Genome Center, University of Tokyo) PRotein Interactions and Molecular Information databasE integrated gene/protein informatics database based on natural language processing http://prime.ontology.ims.u-tokyo.ac.jp:8081/ ProtoArray&reg (Invitrogen) http://www.invitrogen.com/content.cfm?pageid=10400 Protein Interaction Database (Protein Lounge) database lists thousands of human protein-protein interactions created through in-dept research of hundreds of signal transduction pathways http://www.proteinlounge.com/inter_home.asp Protein Interaction Maps - PIMs (Hybrigenics) functional proteomics software platform, dedicated to the exploration of protein pathways PIM's available for Helicobacter pylori, Hepatitis C Virus, Drosophila and TGF-Beta http://pim.hybrigenics.com/pimrider/pimriderlobby/PimRiderLobby.jsp Protein-Protein Interaction Panel using mouse full-length cDNAs (RIKEN, Yokohama Institute) see Suzuki et al., Genome Res. 2001, 11, 1758-1765. [PubMed] http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=11591653&query_hl=5&itool=pubmed_docsum http://genome.gsc.riken.go.jp/ppi/ Protein-Protein Interaction Viewer [+ FANTOM2 Viewer] (RIKEN Yokohama Institute) http://fantom21.gsc.riken.go.jp/PPI/ PSIbase (BioSystems Dept., KAIST & BiO centre) structural interactome map of all proteins http://psibase.kobic.re.kr/ Repair-FunMap (Temple University) database that provides the functional networking of proteins related to DNA repair processes in the cell capable of generating functional maps of interacting proteins around a protein of interest http://guanyin.chem.temple.edu:8080/FunMap/index.html SNAPPIView (University of Dundee) Structures, iNterfaces and Alignments for Protein-Protein Interactions object-oriented database of domain-domain interactions observed in structural data http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp SPIN-PP Server (Columbia University) Surface Properties of INterfaces - Protein Protein interfaces database of all protein-protein interactions in the PDB http://trantor.bioc.columbia.edu/cgi-bin/SPIN/ Yeast Interacting Proteins Database (Kanazawa University) yeast protein interactome view data with a Genetic Network Visualization System http://itolab.cb.k.u-tokyo.ac.jp/Y2H/ http://itolab.cb.k.u-tokyo.ac.jp/webgen/webgen.html Yeast Protein Linkage Map Data (University of Washington) http://depts.washington.edu/sfields/yp_interactions/index.html YPD&#8482 (BIOBASE) Yeast Proteome Database comprehensive knowledge resource for the proteins of S. cerevisiae http://www.biobase-international.com/pages/index.php?id=ypd Predictions ADAN (EMBL) prediction of protein-protein interAction of moDular domAiNs http://adan-embl.ibmc.umh.es AtPID (Northeast Forest University) Arabidopsis Thaliana Protein Interactome Database rich source of information for system-level understanding of gene function and biological processes in A. thaliana integrates data from several bioinformatics prediction methods and manually collected information from the literature contains data relevant to protein-protein interaction, protein subcellular location, ortholog maps, domain attributes and gene regulation http://atpid.biosino.org/ E. Coli Predicted Protein Interactions Database (Universidad Aut&oacutenoma Cantoblanco) in silico two-hybrid system for the prediction of interaction partners to the entire E. coli genome http://www.pdg.cnb.uam.es/i2h/ Fly-DPI ( National Health Research Institutes) statistical model to predict protein interaction networks of Drosophila melanogaster http://flydpi.nhri.org.tw/protein/fly/general_search/ Genes2Networks (Mount Sinai School of Medicine) connecting lists of gene symbols using mammalian protein interactions databases powerful web-based software that can help to interpret lists of genes and proteins can be used to find relationships between genes and proteins from seed lists, and predict additional genes or proteins that may play key roles in common pathways or protein complexes http://actin.pharm.mssm.edu/genes2networks/ HAPPI (Indiana University School of Informatics, Purdue University School of Science) Human Annotated and Predicted Protein Interaction database collected or inferred computationally from public sources http://bio.informatics.iupui.edu/HAPPI/ HPID (Inha University) Human Protein Interaction Database http://wilab.inha.ac.kr/hpid/ ICBS (University of California) Inter-Chain Beta-Sheets database of protein-protein interactions mediated by interchain ß-sheet formation http://contact14.ics.uci.edu/index.html INTERPARE (National Genome Information Center, Korea Research Institute of Bioscience and Biotechnology &amp BiO Centre) protein "interfaceome" database contains large-scale interface data of proteins with known 3D-structures http://interpare.net/ NOXclass (Max-Planck-Institut f&uumlr Informatik) SVM (support vector machine algorithm) classifier identifying protein-protein interaction types http://noxclass.bioinf.mpi-inf.mpg.de/ OPHID (Ontario Cancer Institute & University of Toronto) Online Predicted Human Interaction Database designed to be both a resource for the laboratory scientist to explore known and predicted protein-protein interactions, and to facilitate bioinformatics initiatives exploring protein interaction networks http://ophid.utoronto.ca/ PIBASE (University of California) comprehensive database of structurally defined interfaces between pairs of protein domains http://alto.compbio.ucsf.edu/pibase/ PPIDB (Iowa State University) database of protein-protein interfaces derived from all protein-protein complexes available in the Protein Data Bank http://ppidb.cs.iastate.edu/index.htm Predictome (Boston University) database of putative links between proteins using sequence data of genomes of 44 microorganisms http://predictome.bu.edu/static/sources.html PreSPI (Information and Communications University) PREdiction System for Protein Interaction domain combination based protein interaction prediction system http://prespi.icu.ac.kr/ PRIMOS (BIOMIS, FH Hagenberg) PRotein Interaction and MOlecule Search) database integrated knowledge portal for analysing integrated protein-protein interaction data http://biomis.fh-hagenberg.at/isp/Primos/ PRISM (Koc University) PRotein Interactions by Structural Matching explore protein interfaces and predict protein-protein interactions http://gordion.hpc.eng.ku.edu.tr/prism/ PRODISTIN Web Site (LGPD/IBDM, CNRS) web service to functionally classify genes/proteins from any type of interaction network http://crfb.univ-mrs.fr/webdistin/ Prolinks Database (University of California) collection of inference methods used to predict functional linkages between proteins methods include the Phylogenetic Profile method, which uses the presence and absence of proteins across multiple genomes to detect functional linkages the Gene Cluster method, which uses genome proximity to predict functional linkage Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage http://www.doe-mbi.ucla.edu/Services/MTBreg/prolinks.html SNAPPI-Predict (University of Dundee) Structures, iNterfaces and Alignments for Protein-Protein Interactions protein-protein interaction prediction program http://www.compbio.dundee.ac.uk/SNAPPI/predict.jsp SPIDer (Beijing Normal University) database of predicted protein-protein interaction network in yeast effective method of reconstructing a yeast protein interaction network by measuring relative specificity similarity (RSS) between two Gene Ontology (GO) terms http://cmb.bnu.edu.cn/SPIDer/index.html Related Domain, Pathway and Network Databases BioCarta (BioCarta) charting pathways of life http://www.biocarta.com/genes/index.asp BioCyc (SRI) includes the literature-derived pathway/genome databases Ecocyc (encyclopedia of E. coli genes and metabolism) & MetaCyc (metabolic pathways and enzymes from 150 species) as well as computationally derived genome/pathway databases for 12 species http://biocyc.org CSNDB (NIHS) Cell Signaling Networks DataBase http://www.chem.ac.ru/Chemistry/Databases/CSNDB.en.html DAPID (National Chiao Tung University) Domain Annotated Protein-protein Interaction Database database of domain-annotated protein interactions inferred from three-dimensional (3D) interacting domains of protein complexes in the Protein Data Bank (PDB) http://gemdock.life.nctu.edu.tw/dapid DIMA (MIPS, TUM) Domain Interaction MAp comprehensive resource for functional and physical interactions among conserved protein-domains http://mips.gsf.de/genre/proj/dima2/ DOMINE (University of Texas at Dallas) database of known and predicted protein domain (domain-domain) interactions http://domine.utdallas.edu/cgi-bin/Domine DOQCS (NCBS) Database Of Quantitative Cellular Signaling http://doqcs.ncbs.res.in./ EDGEdb (University of Massachusetts Medical School) C. Elegans Differential Gene Expression database http://edgedb.umassmed.edu/IndexAction.dojsessionid=83C4B5E969161C36F9CFA68A8C0EAF3D EMP (EMP Project Inc.) Enzymes and Metabolic Pathways http://www.empproject.com/about/ HotSprint (KOC University, Turkey) database of computational hot spots in protein interfaces http://prism.ccbb.ku.edu.tr/hotsprint/index.php iHOP (Computational Biology Center, Memorial Sloan-Kettering Cancer Center, USA & Protein Design Group, National Center of Biotechnology, Spain) Information Hyperlinked Over Proteins gene network for navigating the literature http://www.ihop-net.org/UniPub/iHOP/ InCeP (Kazusa DNA Research Institute) database for IntraCellular Pathway based on mKIAA protein-protein interactions http://www.kazusa.or.jp/create/index.jsp InterDom (Laboratories for Information Technology) database of putative INTERacting protein DOMains derived from multiple sources http://interdom.lit.org.sg/ KEGG Kyoto Encyclopedia of Genes and Genomes [*::http://www.genome.ad.jp/kegg/metabolism.htmlMetabolic Pathways | *::http://www.genome.ad.jp/kegg/regulation.htmlRegulatory Pathways] http://www.genome.ad.jp/kegg/ KEGG LIGAND database of chemical compounds and reactions in biological pathways http://www.genome.ad.jp/dbget/ligand.html Kinase Pathway Database (Human Genome Center) integrated database concerning completed sequenced major eukaryotes, which contains the classification of protein kinases and their functional conservation and orthologous tables among species, protein-protein interaction data, domain information, structural information, and automatic pathway graph image interface http://kinasedb.ontology.ims.u-tokyo.ac.jp/ Pathway Database (Protein Lounge) database of protein signaling and metabolic pathways http://www.proteinlounge.com/pathway_home.asp Pfam (Sanger Institute) Protein FAMilies database of alignments and HMM http://www.sanger.ac.uk/Software/Pfam/ PUMA2 (Argonne National Lab) evolutionary analysis of metabolism http://compbio.mcs.anl.gov/puma2/ Roche Applied Science 'Biochemical Pathways' http://www.expasy.org/cgi-bin/search-biochem-index SCOPPI (TU Dresden) Structural Classification Of Protein-Protein Interfaces http://www.scoppi.org/ SMART (EMBL Heidelberg) Simple Modular Architecture Research Tool http://smart.embl-heidelberg.de SPAD (Kyushu University) Signaling PAthway Database http://www.grt.kyushu-u.ac.jp/spad/ SoyBase (Yale University) soybean metabolism http://cgsc.biology.yale.edu/metab.html TRANSCompel (BIOBASE) database of composite regulatory elements affecting gene transciption in eukaryotes [*::http://www.biobase.de/pages/guided_tours/transcompel/tour.htmlGuided Tour] http://www.gene-regulation.com/pub/databases.html#transcompel TRANSPATH (BIOBASE) database on molecular pathways and cellular network modelling [*::http://www.biobase.de/pages/guided_tours/transpath/tour.htmlGuided Tour] http://www.biobase-international.com/pages/index.php?id=transpathdatabases UniHI (Charite - Medical Devision, Humboldt-University zu Berlin) Unified Human Interactome comprehensive database of the computational and experimental based human protein interaction networks http://theoderich.fb3.mdc-berlin.de:8080/unihi/home The Interactive Fly (Society for Developmental Biology) a guide to Drosophila genes and their role in development includes information on *::http://www.sdbonline.org/fly/aimain/5zygotic.htmbiochemical pathways http://www.sdbonline.org/fly/aimain/1aahome.htm Wnt Signaling Pathway (Stanford University Medical Center) http://www.stanford.edu/%7Ernusse/wntwindow.html Yeast Interactome (Boston University) http://structure.bu.edu/rakesh/myindex.html interaction map with valuable information regarding to biochemical processes Yeast Pathways in the Comprehensive Yeast Genome Database (MIPS) http://mips.gsf.de/proj/yeast/CYGD/db/pathway_index.html Webtools APID (Cancer Research Center) Agile Protein Interaction DataAnalyzer interactive web-tool all known experimentally validated protein-protein interactions http://bioinfow.dep.usal.es/apid/index.htm ADVICE (Institute for Infocomm Research) Automated Detection and Validation of Interaction by Co-Evolution prediction and validation of protein-protein interactions http://advice.i2r.a-star.edu.sg/ BioLayout Java (EMBL) automatic graph layout algorithm for similarity and network visualization http://cgg.ebi.ac.uk/services/biolayout/ eFsite (Osaka University) Electrostatic surface of Functional-SITE database for molecular surfaces of proteins' functional sites, displaying the electrostatic potentials and hydrophobic properties together on the Connolly surfaces of the active sites http://ef-site.hgc.jp/eF-site/ Expression Profiler (European Bioinformatics Institute) explores protein interaction data using expression data http://ep.ebi.ac.uk/EP/PPI/ FunSimMat (Max Planck Institute for Informatics) Functional Similarity Matrix comprehensive functional similarity database http://funsimmat.bioinf.mpi-inf.mpg.de/ IntAct Project (European Bioinformatics Institute) database and toolkit for the storage, presentation and analysis of protein interactions http://www.ebi.ac.uk/intact/index.html InterPreTS (EMBL) protein INTERaction PREdiction through Tertiary Structure http://speedy.embl-heidelberg.de/people/patrick/interprets/index.html InterProSurf (University of Texas Medical Branch) web server for predicting the functional sites nonprotein surfaces http://curie.utmb.edu/ InterViewer (Inha University) visualization oflarge-scale protein interaction networks http://interviewer.inha.ac.kr/ InterWeaver (Institute for InfoComm Research) web server of interaction reports http://interweaver.i2r.a-star.edu.sg/ iPPI (National Bioinformatics Center Cuba) infers protein-protein interactions through homology search http://www.bioinfo.cu/iPPI.html IPPRED (Centre de Bioinformatique de Bordeaux) proteins interactions inference server infers interactions through homology search http://cbi.labri.fr/outils/ippred/IS_part_simple.php iSPOT (Universita di Roma) prediction of protein-protein interactions mediated by families of peptide recognition modules http://cbm.bio.uniroma2.it/ispot/ Medusa (EMBL) interface to the *::http://string.embl.de/STRING protein interaction database a general graph visualization tool http://www.bork.embl-heidelberg.de/medusa/ NetAlign (Lab of Protein Crystallography, USTC) a web-based tool for comparison of protein interaction networks http://www1.ustc.edu.cn/lab/pcrystal/NetAlign/ PathBLAST (Whitehead Institute) network alignment and search tool for comparing protein interaction networks across species to identify protein pathways and complexes that have been conserved by evolution http://www.pathblast.org/ PEDANT (GSF) Protein Extraction, Description, and Analysis Tool http://pedant.gsf.de/ PDBSiteScan (Institute of Cytology and Genetics SBRAS) designed for searching 3D protein fragments similar in structure to known active, binding and posttranslational modification sites http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html (Centro Nacional de Biotecnolog&iacutea) contact prediction server http://www.pdg.cnb.uam.es:8081/pdg_contact_pred.htmlPDGcon PIMWalkerTM (Hybrigenics) intercative tool for displaying protein interaction networks http://pim.hybrigenics.com/pimriderext/pimwalker/ PIVOT (Tel Aviv University) Protein Interactions VisualizatiOn Tool http://www.cs.tau.ac.il/~rshamir/pivot/ Protein3D Home (LECB) http://protein3d.ncifcrf.gov/tsai/frame/main.html Protein-Protein Interaction Server (University College London) 3D structures http://www.biochem.ucl.ac.uk/bsm/PP/server/server_help.html SCOWLP (TU Dresden) Structural Characterization Of Water, Ligands and Proteins web-based relational database describing PDB interface interactions at atom, residue and domain level http://www.scowlp.org/ SPIN-PP Server (Columbia University) Surface Properties of INterfaces - Protein Protein interfaces database of all protein-protein interactions in the Protein Data Bank http://trantor.bioc.columbia.edu/cgi-bin/SPIN/ STRING (EMBL) Search Tool for the Retrieval of INteracting Genes/proteins database of known and predicted protein-protein interactions for a large number of organisms interactions include direct (physical) and indirect (functional) associations data are derived from four sources: genomic context, high-throughput experiments, (conserved) coexpression and previous knowledge http://string.embl.de/ YETI (University Edinburgh) Yeast Exploration Tool Integrator workbench tool for visualization/analysis of post-genomic data sets available for Saccharomyces cerevisiae http://www.yetibio.com/ References: