HARMONY: a server for the assessment of protein structures

Abstract

Protein structure validation is an important step in computationalmodelingandstructure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (Φ,Ψ) 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/.