# 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
* PIMWalker$^{TM}$ (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:

* ↑ http://www.imb-jena.de/jcb/ppi