Proteomics/Protein - Protein Interactions/Jena Links

Page Edited and Updated by: Dan Surdyk E-mail: dfs6389@rit.edu

This Section:

Links from the Jena Center for Bioinformatics Page
Please note that the following page of references was quoted from the following online source:

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/