SMS: Sequence, Motif and Structure – A Database on the Structural Rigidity of Peptide Fragments in Non-Redundant Proteins

Article type: Research Article

Authors: Balamurugan, Bhagavathimuthu | Roshan, M.N.A. Mohd. | Michael, Daliah | Ambaree, Majumder | Divya, Subramanyam | Keerthana, Hanumanthagowda | Seemanthini, Mahadev | Sekar, Kanagaraj^;

Affiliations: Bioinformatics Centre | Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560 012, India

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Abstract: Structure prediction methods aim to identify the relationship between the amino acid sequence of an unknown protein and information comprised in databases of known protein structures. Towards this end, we created a database by combining the amino acid sequences and the corresponding three-dimensional atomic coordinates for all the 25% non-redundant protein chains available in the Protein Data Bank. It contains information about the peptide fragments that are 5 to 10 residues long. In addition, options are provided for the users to visualize the individual motifs and the superposed fragments in the client machine. Further, useful functionalities are provided to look for similar sequence motifs in all the sequence databases like PDB, 90% non-redundant protein chains, Genome database, PIR and Swiss-Prot. The database is being updated at regular intervals and the same can be accessed over the World Wide Web interface at the following URL: http://pranag.physics.iisc.ernet.in/sms/.

Keywords: Protein sequences, database, structural rigidity, Protein Data Bank, genome sequences, superposition, World Wide Web, non-redundant structures

Journal: In Silico Biology, vol. 6, no. 3, pp. 229-235, 2006