The MIPS Mammalian Protein-Protein Interaction Database

The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions.

Search the database

To suit different users needs we provide a variety of interfaces to search the database:

Expert interface – Simple but powerful boolean query language.
PPI search form – Easy to use PPI search
Protein search – Just find proteins of interest in the database

Background

Protein-protein interactions (PPI) represent a pivotal aspect of protein function. Almost every cellular process relies on transient or permanent physical binding of two or more proteins in order to accomplish the respective task. Comprehensive databases of PPI in Saccharomyces cerevisiae have proved to be invaluable resources for both bioinformatics and experimental research and are used heavily in the scientific community.

Although yeast is a well established model organism, not all interactions in higher eukaryotes have equivalent counterparts in unicellular systems. Currently, publicly available PPI databases contain comparatively few entries from mammals so we embarked on building a high-quality, manually curated database of protein-protein interactions in mammals.

Conditions of use

You are free to use the database as you please including full download of the dataset for your own analyses as long as you cite the source properly:

Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stümpflen V, Mewes HW, Ruepp A, Frishman D
The MIPS mammalian protein-protein interaction database
Bioinformatics 2005; 21(6):832-834; [Epub 2004 Nov 5] doi:10.1093/bioinformatics/bti115

Other PPI resources

There are plenty of interesting databases and other sites on protein-protein interactions. Currently we are aware of the following PPI resources:

Resource Comments

APID Agile Protein Interaction DataAnalyzer (Cancer Research Center, Salamanca, Spain)

BIND Biomolecular INteraction Network Database at the University of Toronto, Canada. No species restriction

CYGD PPI section of the Comprehensive Yeast Genome Database. Manually curated comprehensive S. cerevisiae PPI database at MIPS

DIP Database of Interacting Proteins at UCLA. No species restriction.

GRID General Repository for Interaction Datasets. Mount Sinai Hospital, Toronto, Canada

HIV Interaction DB Interactions between HIV and host proteins.

HPRD The Human Protein Reference Database. Institute of Bioinformatics, Bangalore, India and Johns Hopkins University, Baltimore, MD, USA.

HPID Human Protein Interaction Database. Department of computer Science and Information Engineering Inha University, Inchon, Korea

iHOP iHOP (Information Hyperlinked over Proteins). Protein association network built by literature mining

IntAct Protein interaction database at EBI. No species restriction.

InterDom Database of putative interacting protein domains. Institute for InfoComm Research, Singapore.

JCB PPI site at the Jena Centre for Bioinformatics, Germany

MetaCore Commercial software suite and database. Manually curated human PPIs (among other things). GeneGo

MINT Molecular INTeraction database at the Centro di Bioinformatica Moleculare, Universita di Roma, Italy.

MRC PPI links Commented list of links to PPI databases and resources maintained at the MRC Rosalind Franklin Cetre for Genomics Research, Cambridge, UK

OPHID The Online Predicted Human Interaction Database. Ontario Cancer Institute and University of Toronto, Canada.

Pawson Lab Information on protein-interaction domains.

PDZbase Database of PDZ mediated protein-protein interactions.

Predictome Predicted functional associations and interactions. Boston University.

Protein-Protein Interaction Server Analysis of protein-protein interfaces of protein complexes from PDB. University College of London, UK.

PathCalling Proteomics and PPI tool/database. CuraGen Corporation.

PIM Hybrigenics PPI data and tool, H. pylori. Free academic license available

RIKEN Experimental and literature PPIs in mouse.

STRING Protein networks based on experimental data and predictions at EMBL.

YPD "BioKnowledge Library" at Incyte Corporation. Manually curated PPI data from S. cerevisiae. Proprietary.

Resource	Comments
APID	Agile Protein Interaction DataAnalyzer (Cancer Research Center, Salamanca, Spain)
BIND	Biomolecular INteraction Network Database at the University of Toronto, Canada. No species restriction
CYGD	PPI section of the Comprehensive Yeast Genome Database. Manually curated comprehensive S. cerevisiae PPI database at MIPS
DIP	Database of Interacting Proteins at UCLA. No species restriction.
GRID	General Repository for Interaction Datasets. Mount Sinai Hospital, Toronto, Canada
HIV Interaction DB	Interactions between HIV and host proteins.
HPRD	The Human Protein Reference Database. Institute of Bioinformatics, Bangalore, India and Johns Hopkins University, Baltimore, MD, USA.
HPID	Human Protein Interaction Database. Department of computer Science and Information Engineering Inha University, Inchon, Korea
iHOP	iHOP (Information Hyperlinked over Proteins). Protein association network built by literature mining
IntAct	Protein interaction database at EBI. No species restriction.
InterDom	Database of putative interacting protein domains. Institute for InfoComm Research, Singapore.
JCB	PPI site at the Jena Centre for Bioinformatics, Germany
MetaCore	Commercial software suite and database. Manually curated human PPIs (among other things). GeneGo
MINT	Molecular INTeraction database at the Centro di Bioinformatica Moleculare, Universita di Roma, Italy.
MRC PPI links	Commented list of links to PPI databases and resources maintained at the MRC Rosalind Franklin Cetre for Genomics Research, Cambridge, UK
OPHID	The Online Predicted Human Interaction Database. Ontario Cancer Institute and University of Toronto, Canada.
Pawson Lab	Information on protein-interaction domains.
PDZbase	Database of PDZ mediated protein-protein interactions.
Predictome	Predicted functional associations and interactions. Boston University.
Protein-Protein Interaction Server	Analysis of protein-protein interfaces of protein complexes from PDB. University College of London, UK.
PathCalling	Proteomics and PPI tool/database. CuraGen Corporation.
PIM	Hybrigenics PPI data and tool, H. pylori. Free academic license available
RIKEN	Experimental and literature PPIs in mouse.
STRING	Protein networks based on experimental data and predictions at EMBL.
YPD	"BioKnowledge Library" at Incyte Corporation. Manually curated PPI data from S. cerevisiae. Proprietary.

If we forgot to list your favorite PPI resource or you are providing one yourself please let us know - we will be happy to include it.

PPI related software

Resource	Comments
aiSee	Commercial graph layout software
Cytoscape	Open source software for visualization of PPI networks and data integration
graphviz	Graph layout software

Download

You can get the full dataset here (PSI-MI format).

Acknowledgements

This work is funded by a grant from the German Federal Ministry of Education and Research. It is part of the initiative "Bioinformatics for the Functional Analysis of Mammalian Genomes" (BFAM).

Contact

For questions, criticism, praise and suggestions please contact Dr. Philipp Pagel or Dr. Dmitrij Frishman.