- Article -
| In Silico Biology 6, 0021 (2006); ©2006, Bioinformation Systems e.V. |
SMS: Sequence, Motif and Structure - A database on the structural rigidity of peptide fragments in non-redundant proteins
Bhagavathimuthu Balamurugan1, M. N. A. Mohd. Roshan1, Daliah Michael1, Majumder Ambaree1, Subramanyam Divya1, Hanumanthagowda Keerthana1, Mahadev Seemanthini1 and Kanagaraj Sekar1,2,*
1 Bioinformatics Centre
2 Supercomputer Education and Research Centre
Indian Institute of Science, Bangalore 560 012, India
* Corresponding author
Email: sekar@physics.iisc.ernet.in, sekar@serc.iisc.ernet.in
Edited by E. Wingender; received January 10, 2006; revised March 23 & April 07, 2006; accepted April 09, 2006; published April 19, 2006
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