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.
Bibliographical noteFunding Information:
G.P. and P.N.S. acknowledge the financial support offered by A*Star (Agency for Science, Technology and Research). R.S. acknowledges Wellcome Trust, UK and National Centre for Biological Sciences (TIFR) for financial and infrastructural support. S.C. acknowledges Intramural Research Program of the National Library of Medicine at NIH/DHHS. Funding to pay the Open Access publication charges for this article was provided by Wellcome Trust, U.K.
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