BSSB:BLASTServer for Structural Biologists

Abstract

The Basic Local Alignment Search Tool (BLAST) is one of the most widely used sequence alignment programs with which similarity searches, for both protein and nucleic acid sequences, can be performed against large databases at high speed. A large number of tools exist for processing BLAST output, but none of them provide three‐dimensional structure visualization. This shortcoming has been addressed in the proposed tool BLAST Server for Structural Biologists (BSSB), which maps a BLAST output onto the three‐dimensional structure of the subject protein. The three‐dimensional structure of the subject protein is represented using a three‐color coding scheme (identical: red; similar: yellow; and mismatch: white) based on the pairwise alignment obtained. Thus, the user will be able to visualize a possible three‐dimensional structure for the query protein sequence. This information can be used to gain a deeper insight into the sequence–structure correlation. Furthermore, the additional structure‐level information enables the user to make coherent and logical decisions regarding the type of input model structure or fragment that can be used for molecular replacement calculations. This tool is freely available to all users at http://bioserver1.physics.iisc.ernet.in/bssb/.

MRPC (Missing Regions in Polypeptide Chains): a knowledgebase

“…The quality of the data present in the PDB is required to be extremely high (Dodson et al, 1998) as these data serve as input to create various powerful tools and knowledgebases/ databases, which are in turn useful for researchers working in the areas of structural bioinformatics, biochemistry and biophysics (Carugo & Pongor, 2002;Hemavathi et al, 2010;Uthayakumar et al, 2011). Further, these data (sequence and structure) are used heavily in data-mining studies to percolate useful information to derive more knowledge to solve unknown structures (Gowri Shankar et al, 2007;Ranjani et al, 2008;Kanaujia & Sekar, 2009;Sabarinathan et al, 2011;Dhanasekaran et al, 2013).…”