Proteomics/Protein - Protein Interactions/Jena Links

Databases	Protein Interactions	Cross-linking
	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: ^[1]

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/