Rapid chain tracing of polypeptide backbones in electron-density maps

doi:10.1107/S0907444910000272

Title: Rapid chain tracing of polypeptide backbones in electron-density maps

Journal Article · Mon Mar 01 00:00:00 EST 2010 · Acta Crystallographica. Section D: Biological Crystallography

DOI:https://doi.org/10.1107/S0907444910000272· OSTI ID:22347930

Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov ^[1]

Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)

A method for rapid chain tracing of polypeptide backbones at moderate resolution is presented. 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{sup 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{sup 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{sup α} atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality.

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OSTI ID:: 22347930

Journal Information:: Acta Crystallographica. Section D: Biological Crystallography, Vol. 66, Issue Pt 3; Other Information: PMCID: PMC2827349; PMID: 20179340; PUBLISHER-ID: dz5184; OAI: oai:pubmedcentral.nih.gov:2827349; Copyright (c) Terwilliger 2010; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449

Country of Publication:: Denmark

Language:: English

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