What is InterPro?
InterPro is a resource that provides functional analysis of protein sequences by classifying them into families and predicting the presence of domains and important sites. To classify proteins in this way, InterPro uses predictive models, known as signatures, provided by several different databases (referred to as member databases) that make up the InterPro consortium.
What is InterProScan?
InterProScan is the software package that allows sequences to be scanned against InterPro's signatures (more information about InterProScan).
Why is InterPro useful?
InterPro combines signatures from multiple, diverse databases into a single searchable resource, reducing redundancy and helping users interpret their sequence analysis results. By uniting the member databases, InterPro capitalises on their individual strengths, producing a powerful diagnostic tool and integrated resource.
Who uses InterPro?
InterPro is used by research scientists interested in the large-scale analysis of whole proteomes, genomes and metagenomes, as well as researchers seeking to characterise individual protein sequences. Within the EBI, InterPro is used to help annotate protein sequences in UniProtKB. It is also used by the Gene Ontology Annotation group to automatically assign Gene Ontology terms to protein sequences.
InterPro is updated approximately every 8 weeks. Our release notes pages contain information about what has changed in each update.
How to cite / publications
To cite InterPro, please refer to the following publication:
Alex L Mitchell, Teresa K Attwood, Patricia C Babbitt, Matthias Blum, Peer Bork, Alan Bridge, Shoshana D Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew I Fraser, Julian Gough, David R Haft, Hongzhan Huang, Ivica Letunic, Rodrigo Lopez, Aurélien Luciani, Fabio Madeira, Aron Marchler-Bauer, Huaiyu Mi, Darren A Natale, Marco Necci, Gift Nuka, Christine Orengo, Arun P Pandurangan, Typhaine Paysan-Lafosse, Sebastien Pesseat, Simon C Potter, Matloob A Qureshi, Neil D Rawlings, Nicole Redaschi, Lorna J Richardson, Catherine Rivoire, Gustavo A Salazar, Amaia Sangrador-Vegas, Christian J A Sigrist, Ian Sillitoe, Granger G Sutton, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Siew-Yit Yong and Robert D Finn (2019). InterPro in 2019: improving coverage, classification and access to protein sequence annotations. Nucleic Acids Research, Jan 2019; doi: 10.1093/nar/gky1100
To cite InterProScan, please refer to:
Philip Jones, David Binns, Hsin-Yu Chang, Matthew Fraser, Weizhong Li, Craig McAnulla, Hamish McWilliam, John Maslen, Alex Mitchell, Gift Nuka, Sebastien Pesseat, Antony F. Quinn, Amaia Sangrador-Vegas, Maxim Scheremetjew, Siew-Yit Yong, Rodrigo Lopez, and Sarah Hunter (2014). InterProScan 5: genome-scale protein function classification. Bioinformatics, Jan 2014; doi:10.1093/bioinformatics/btu031
The list of all our recent publications can be found in the publication section.
The InterPro Team
The InterPro team homepage can be found on the EBI staff pages.
The InterPro Consortium
The following databases make up the InterPro Consortium:
|CATH-Gene3D database describes protein families and domain architectures in complete genomes. Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity. Mapping of predicted structure and sequence domains is undertaken using hidden Markov models libraries representing CATH and Pfam domains. CATH-Gene3D is based at University College, London, UK.|
|CDD is a protein annotation resource that consists of a collection of annotated multiple sequence alignment models for ancient domains and full-length proteins. These are available as position-specific score matrices (PSSMs) for fast identification of conserved domains in protein sequences via RPS-BLAST. CDD content includes NCBI-curated domain models, which use 3D-structure information to explicitly define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases.|
|MobiDB offers a centralized resource for annotations of intrinsic protein disorder. The database features three levels of annotation: manually curated, indirect and predicted. The different sources present a clear tradeoff between quality and coverage. By combining them all into a consensus annotation, MobiDB aims at giving the best possible picture of the "disorder landscape" of a given protein of interest.|
|HAMAP stands for High-quality Automated and Manual Annotation of Proteins. HAMAP profiles are manually created by expert curators. They identify proteins that are part of well-conserved proteins families or subfamilies. HAMAP is based at the SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.|
|PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function, as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences. PANTHER is based at at University of Southern California, CA, US.|
|Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Pfam is based at EMBL-EBI, Hinxton, UK.|
|PIRSF protein classification system is a network with multiple levels of sequence diversity from superfamilies to subfamilies that reflects the evolutionary relationship of full-length proteins and domains. PIRSF is based at the Protein Information Resource, Georgetown University Medical Centre, Washington DC, US.|
|PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family or domain. PRINTS is based at the University of Manchester, UK.|
|ProDom protein domain database consists of an automatic compilation of homologous domains. Current versions of ProDom are built using a novel procedure based on recursive PSI-BLAST searches. ProDom is based at PRABI Villeurbanne, France.|
|PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family a new sequence belongs. PROSITE is base at the Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland.|
|SFLD (Structure-Function Linkage Database) is a hierarchical classification of enzymes that relates specific sequence-structure features to specific chemical capabilities.|
|SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. SMART is based at at EMBL, Heidelberg, Germany.|
|SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain and aims to represent the entire SCOP superfamily that the domain belongs to. SUPERFAMILY is based at the University of Bristol, UK.|
|TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, hidden Markov models (HMMs) and annotation, which provides a tool for identifying functionally related proteins based on sequence homology. TIGRFAMs is based at the J. Craig Venter Institute, Rockville, MD, US.|
Current InterPro Funding
InterPro is supported by EMBL, with additional funding gratefully received from the Biotechnology and Biological Sciences Research Council (BBSRC grants BB/L024136/1 and BB/N00521X/1) and the Wellcome Trust (grant 108433/Z/15/Z).
▸ Previous InterPro Funding
|InterPro was funded by the award of grant number QLRI-CT-2000-00517 and in part by grant number QLRI-CT-2001000015 from the European Union under the RTD program "Quality of Life and Management of Living Resources".|
|InterPro was funded by grant number 213037 from the European Union under the program "FP7 capacities: Scientific Data Repositories". The working title for the project is IMproving Protein Annotation and Co-ordination using Technology (IMPACT).|
|InterPro was also part of the MRC-funded eFamily project.|
We occasionally have positions available, which are listed on the EMBL-EBI jobs site. Please check the site for details.