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Bioinformatics Advance Access published online on January 19, 2007
Bioinformatics, doi:10.1093/bioinformatics/btl679
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SMotif: A server for structural motifs in proteins.

Ganesan Pugalenthi 1, P.N. Suganthan 1,*, R. Sowdhamini 2,* and Saikat Chakrabarti 3,*

1 School of Electrical and Electronic Engineering, Nanyang Technological University Singapore, 639798.
2National Centre for Biological Sciences, Bangalore 560 065, India.
3National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA.

* Authors for correspondence. P.N. Suganthan, R. Sowdhamini and Saikat Chakrabarti, E-mail: chakraba{at}mail.nih.gov, mini{at}ncbs.res.in and EPNSugan{at}ntu.edu.sg.


  Abstract

Summary: SMotif is a server that identifies important structural segments or motifs for a given protein structure(s) based on conservation of both sequential as well as important structural features such as solvent inaccessibility, secondary structural content, hydrogen bonding pattern and residue packing. This server also provides three-dimensional orientation patterns of the identified motifs in terms of inter-motif distances and torsion angles. These motifs may form the common core and therefore, can also be employed to design and rationalize protein engineering and folding experiments.

Availability: SMotif server is available via the URL http://caps.ncbs.res.in/SMotif/index.html.

Associate Editor: Dmitrij Frishman

Received on October 27, 2006; revised on December 15, 2006; accepted on January 5, 2007

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