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Bioinformatics Advance Access originally published online on January 19, 2007
Bioinformatics 2007 23(5):637-638; doi:10.1093/bioinformatics/btl679
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

SMotif: a server for structural motifs in proteins

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

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

*To whom correspondence should be addressed.


  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.

Contact: chakraba{at}mail.nih.gov, mini{at}ncbs.res.in or EPNSugan{at}ntu.edu.sg

Supplementary information: Supplementary data are available at Bioinformatics online.

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

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Home page
 Nucleic Acids ResHome page
G. Pugalenthi, P. N. Suganthan, R. Sowdhamini, and S. Chakrabarti
MegaMotifBase: a database of structural motifs in protein families and superfamilies
Nucleic Acids Res., January 1, 2008; 36(suppl_1): D218 - D221.
[Abstract] [Full Text] [PDF]


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