Proteomics/Protein - Protein Interactions/Jena Links

From Wikibooks, open books for an open world
< Proteomics‎ | Protein - Protein Interactions
Jump to: navigation, search
« Protein Interactions
Jena Links
»
Databases Cross-linking

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


This Section:


Links from the Jena Center for Bioinformatics Page[edit]

Please note that the following page of references was quoted from the following online source: [1]

Experimental Data[edit]

  • 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[edit]

  • 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[edit]

  • 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[edit]

  • 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 onprotein 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 similiar 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:[edit]

  1. http://www.imb-jena.de/jcb/ppi