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Title: 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. 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 formore » rapid evaluation of electron-density map quality.« less

Authors:
 [1]
  1. Los Alamos National Laboratory, Los Alamos, NM 87545 (United States)
Publication Date:
OSTI Identifier:
22347930
Resource Type:
Journal Article
Journal Name:
Acta Crystallographica. Section D: Biological Crystallography
Additional Journal Information:
Journal Volume: 66; Journal 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); Journal ID: ISSN 0907-4449
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; CHAINS; DENSITY; DISTANCE; ELECTRON DENSITY; ELECTRONS; FASTENING; RESOLUTION; VELOCITY

Citation Formats

Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov. Rapid chain tracing of polypeptide backbones in electron-density maps. Denmark: N. p., 2010. Web. doi:10.1107/S0907444910000272.
Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov. Rapid chain tracing of polypeptide backbones in electron-density maps. Denmark. doi:10.1107/S0907444910000272.
Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov. Mon . "Rapid chain tracing of polypeptide backbones in electron-density maps". Denmark. doi:10.1107/S0907444910000272.
@article{osti_22347930,
title = {Rapid chain tracing of polypeptide backbones in electron-density maps},
author = {Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov},
abstractNote = {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.},
doi = {10.1107/S0907444910000272},
journal = {Acta Crystallographica. Section D: Biological Crystallography},
issn = {0907-4449},
number = Pt 3,
volume = 66,
place = {Denmark},
year = {2010},
month = {3}
}