Recent Advances in Protein Bioinformatics

Abstract

The bioinformatics branch deals with the application of high-order computational and analytical tools to capture and analyze biological information. Applying this to the branch of protein study or proteomics offers the management, data elaboration and integration of new software packages and algorithms. A database is the collection of sequence and structure information that is featured, annotated and retrievable. The data can be searchable using a search engine, updated periodically and even cross-referenced. This chapter thus deals with the current scenario of protein bioinformatics in terms of recent advances in protein sequence, structure and interaction databases along with specialised dedicated databases for model organisms. The protein sequence database has complimented upon UniProtKB as neXtProt (https://www.nextprot.org), a human protein knowledgebase generating data on proteomics (85%) and genetic variations in humans. The recent development in the field of protein-degrading enzymes in the MEROPS database publicly available at http://www.ebi.ac.uk/merops/ is an integrated source of all sets of information about peptidases. PDBFlex database (http://pdbflex.org) provides information on the flexibility of protein structures by analysing their structural differences and clustering them according to their similarities. Proteins with therapeutic and signaling properties have been designed along with fluorescent proteins with novel or enhanced utility using novel structure prediction databases. Developments in the field of protein bioinformatics have led to the establishment of new databases specified to protein-protein interactions (PPIs). P2Rank is a fast, accurate and stable predictor of ligand binding sites in proteins and in the near future can be used for new allosteric site predictions. APID is a comprehensive repository of curated ‘protein interactomes’ accessible at (http://apid.dep.usal.es). It includes 500 experimentally detected PPIs of more than 1100 organisms from nearly 30 species. The latest version of STRING (11.0) features a genome dataset as input with easy visualisation of interaction network (interactome) and thus performs gene-set enrichments. The Integrated Interactions Database (IID) is another comprehensive context-specific human PPI network available at http://ophid.utoronto.ca/iid. A recent update shows the involvement of 18 species with 4.8 million PPIs in 133 tissues. IID provides unique functionality with reduced false negatives and even supports non-human species.