A Web Database IR-PDB for Sequence Repeats of Proteins in the Protein Data Bank

Abstract

Amino acid repeats play significant roles in the evolution of structure and function of many large proteins. Analysis of internal repeats of protein with known structure helps to understand the importance of repeats of the protein. A database IR-PDB for repeats in sequence of the proteins in the PDB has been developed for the analysis of impact of repeats in proteins. Using the state of the art repeat detection method RADAR, internal repeats in 148202 sequences out of 285714 sequences belonging to 115031 PDB structures were detected. The identified sequence repeats were annotated with secondary structural information with a view to analyze the structural consequence and conservation of the repeats. The tertiary structure of the repeats and their functional involvements can be found out through web links to PDB, PDBsum and Pfam. IR-PDB is systematically annotated for the proteins in the PDB with sequence repeats and their structure with the possibility to access the dataset interactively through web services.