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Nucleic Acids Research 2006 34(Web Server issue):W231-W234; doi:10.1093/nar/gkl314
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© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

HARMONY: a server for the assessment of protein structures

G. Pugalenthi, K. Shameer, N. Srinivasan1 and R. Sowdhamini*

National Centre for Biological Sciences (TIFR), GKVK Campus Bellary Road Bangalore 560 065, India 1 Molecular Biophysics Unit, Indian Institute of Science Bangalore 560 012, India

*To whom correspondence should be addressed. Tel: +91 80 23636421, ext. 4240; Fax: +91 80 23636462; Email: mini{at}ncbs.res.in

Received February 9, 2006. Revised March 1, 2006. Accepted April 11, 2006.

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran ({varphi},{psi}) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at http://caps.ncbs.res.in/harmony/


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