INTERPRO

The UniProt KB is an automatically and manually annotated protein database drawn from translation of DDBJ/EMBL-Bank/GenBank coding sequences and directly sequenced proteins. Each sequence receives a imique, stable identifier allowing unambiguous identification of any protein across datasets. The KB also provides cross-references to external data collections such as the underlying DNA sequence entries in the DDBJ/EMBL-Bank/GenBank nucleotide sequence databases, 2D PAGE and 3D protein structure databases, various protein domain 

It is clearly desirable that public domain data such as that published in peer-reviewed journals should be accompanied by a defined set of information about the experiment and that all this information and the results obtained be deposited where it is available to all users. A MIAPE-compliant repository will contain sufficient information to allow users to, in principle, recreate any of the experiments stored within it and where possible, the information will be organized in a manner reflecting the structure of the experimental procedures that generated it. 

The PSTMS mzData interchange format is being written to allow both the exchange of experimental data from proteomics experiments involving mass spectrometry and also, with cooperation from instrumentation and search engine manufacturers, to enable researchers to generate data in such a standard directly 

The published version of the PSI-MS XML data interchange format also gives access to tools which allow the user to both convert from mass spectrometry text formats to the PSI-MS XML format and to view and browse stored data in PSI-MS XML format (Pedrioli et al., 2004). 

At an initial HUPO-PSI-sponsored meeting of this group it was decided that the approach to designing such a format should be multilayered, with Level 1 designed to fulfil basic requirements and be suitable for rapid implementahon. Subsequent levels will supply further complexity and flexibility, for example the ability to deal with other interactors such as nucleic acids. Wherever possible, the potential values of attributes in the data model are defined by controlled vocabularies researchers may also ascribe confidence levels to the data at various points throughout the data entry process and add free comments in appropriate places. 

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InterPro (http //www.ebi.ac.uk/interpro), database of protein families, domains, and functional sites allows prediction of the function or structure of a new protein on the basis of its sequence homology to sequences of known proteins. 

The EU funded Interpro project is a collaboration between many of the domain family databases and the SWISS-PROT sequence database. The Interpro collaboration aims to have a centralized annotation resources to reduce the amount of duplication between the database re-... 

There are many different domain database resources, each with their own priorities and strengths. There is currently no effective way to search them all with a single query. Several should be tested to get the most complete results possible. The Interpro collaboration should facilitate the creation of methods to query all the major domain databases in a single action. 

When a novel homology domain has been discovered, it is possible to store the corresponding domain descriptor (profile or HMM) in a number of dedicated domain databases, which can be used to analyze newly identified sequences for their domain content [9, 10]. Several competing domain- and motif-databases exist, including PROSITE, PFAM, SMART, and Superfam, which contain descriptors for most, if not all, of the known domains involved in the ubiquitin system [11-14]. Recently, a new meta-database named INTERPRO has been established, which tries to combine the descriptors of several domain databases under a single user interface [15]. Pointers to the very useful search engines of the domain databases are provided in Table 12.1. 

Data sources Expasy and InterPro, and NCBI databases, accessed August 2002. 

InterProScan - an integration platform for the signature - recognition methods in InterPro. Bioinformatics 17, 847-848. 

As mentioned in Chapter 2 for the description of our Y2H library screening procedure, what we obtained after a bioinformatics analysis is the location of the interacting domain within the bait or the prey protein. In reality, we do not measure interaction between full length proteins but between domains within proteins which is a closer representation of an in vivo interaction where only some key fragments of each protein interact with one another in space. These domains were called Selected Interacting Domain or SID. It is therefore clear that bioinformatics sequence analysis that compare SIDs obtained from Y2H experiments with Interpro domains can lead to very interesting observation regarding the domain keen to interact and can help to discriminate more specifically true and false positives. 

Figure 3. Hierarchical domain clustering of MASC proteins. Interpro domains in MASC proteins occurring more than once in the MASC dataset were clustered. Discrete clusters (grey boxes) were annotated with the protein class of which the majority proteins belonged to. Clusters are formed from co-occurrence of two or more domains characteristic of a protein class...

Mulder NJ, Apweiler R, Attwood TK et al. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res 2003 31(1) 315 18. 

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