Rapid chain tracing of polypeptide backbones in electron-density maps

Abstract

A method for rapid chain tracing of polypeptide backbones at moderate resolution is presented.

Abstract

A method for the rapid tracing of polypeptide backbones has been developed. The method creates an approximate chain tracing that is useful for visual evaluation of whether a structure has been solved and for use in scoring the quality of electron-density maps. The essence of the method is to (i) sample candidate C ^α positions at spacings of approximately 0.6 Å along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate C ^α positions, (iii) score the nonapeptides and choose the highest scoring ones, and (iv) find the longest chains that can be made by connecting nonamers. An indexing and storage scheme that allows a single calculation of most distances and density values is used to speed up the process. The method was applied to 42 density-modified electron-density maps at resolutions from 1.5 to 3.8 Å. A total of 21 428 residues in these maps were traced in 24 CPU min with an overall r.m.s.d. of 1.61 Å for C ^α atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality.