HARMONY: a server for the assessment of protein structures

Abstract

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/

Figure 1

Flowchart representing the steps involved in structure validation for a given query.

Figure 2

Structure validation using HARMONY server. (a) Calibration plot applied on six proteins. Actual harmony propensity score plotted as a function of protein residue length. Points marked in yellow correspond to representative members of proteins in PDB of different lengths used for calibration (Supplementary material). Circle represents correct protein models (1mcp (•), 4fd1 (•), 1y4o (•)). Asterisk represents incorrect models (Deliberate misfold of 1mcp (*), 2fd1 (*), 1tgq (*)). Incorrect models attain low scores than correct models. (b) HARMONY substitution scores are mapped on the immunoglobulin structure (1mcp) in relation to the reverse sequence as a control. (c) Same as (b) but for the deliberate misfold of 1mcp. This model has larger regions of errors in comparison to the correct model (1mcp). (d) Comparison of HARMONY substitution scores of actual and reverse sequence mapped on the 3D structure of E.coli single-stranded DNA-binding protein (1qvc). Residues 52–53, 104–110 and 115–140 are marked with different colors (red, orange and yellow) depending upon the degree of local error.