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Nucleic Acids Research Advance Access originally published online on October 11, 2007
Nucleic Acids Research 2008 36(Database issue):D218-D221; doi:10.1093/nar/gkm794
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Nucleic Acids Research, 2008, Vol. 36, Database issue D218-D221
© 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.

Articles

MegaMotifBase: a database of structural motifs in protein families and superfamilies

Ganesan Pugalenthi1, P. N. Suganthan1, R. Sowdhamini2,* and Saikat Chakrabarti3

1School of Electrical and Electronic Engineering, Nanyang Technological University, Singapore 639798, Singapore, 2National Centre for Biological Sciences, UAS-GKVK Campus, Bellary Road, Bangalore 560 065, India and 3National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

* To whom correspondence should be addressed. Tel: +91-80-23666250; Fax: +91-80-3636662; Email: mini{at}ncbs.res.in Correspondence may also be addressed to Saikat Chakrabarti. Tel: 301-594-6474; Email: chakraba{at}mail.nlm.nih.gov

Received August 14, 2007. Revised September 16, 2007. Accepted September 17, 2007.

Structural motifs are important for the integrity of a protein fold and can be employed to design and rationalize protein engineering and folding experiments. Such conserved segments represent the conserved core of a family or superfamily and can be crucial for the recognition of potential new members in sequence and structure databases. We present a database, MegaMotifBase, that compiles a set of important structural segments or motifs for protein structures. Motifs are recognized on the basis of both sequence conservation and preservation of important structural features such as amino acid preference, solvent accessibility, secondary structural content, hydrogen-bonding pattern and residue packing. This database provides 3D orientation patterns of the identified motifs in terms of inter-motif distances and torsion angles. Important applications of structural motifs are also provided in several crucial areas such as similar sequence and structure search, multiple sequence alignment and homology modeling. MegaMotifBase can be a useful resource to gain knowledge about structure and functional relationship of proteins. The database can be accessed from the URL http://caps.ncbs.res.in/MegaMotifbase/index.html


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