Protein Databases: Operations, Possibilities and Challenges

Abstract

Abstract The information on protein function, as essential component of biological systems, is essential for the development of biology and biomedicine. The information on proteins is organised in databases that store their sequences, domain organisation, three‐dimensional structures, posttranslational modifications, interactions, molecular functions and other protein features. This information is combined with the proper bioinformatics methods to address complex biological problems. The annotation of splice isoforms is used as a current example of the use of information from central protein databases. Instead of offering a mere catalogue of the many protein databases, which status is periodically reviewed and maintained in ‘The Molecular Biology Database Collection’ ( http://www.oxfordjournals.org/nar/database/c/ ), this article reviews the operations necessary to organise and make openly accessible their information as part of the complex ecosystems of bioinformatics infrastructures. Finally, this article revises the main challenges that their sustainability represents. Key Concepts: Functional annotation is a process of assigning function to a protein based on the experimental evidence published in the literature or transferred from other proteins with similar sequences. Process of adding information to database entries by groups of experts typically associated to large databases is known as database curation. Information transfer is a process of assigning functions or functional characteristics to protein sequences based on the annotations of similar – in most cases orthologos – sequences. Combining annotations from different publications and database to produce a representative description of protein characteristics and functional properties is known as information integration. Bioinformatics infrastructure is the collection of databases, bioinformatics methods, and computational resources that provide the essential support to the work of biologists.