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Rapid chain tracing of polypeptide backbones in electron-density maps

Rapid chain tracing of polypeptide backbones in electron-density maps 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 positions at spacings of approximately 0.6 A along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate C 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 A. 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 A for C atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Acta Crystallographica Section D: Biological Crystallography International Union of Crystallography

Rapid chain tracing of polypeptide backbones in electron-density maps

Rapid chain tracing of polypeptide backbones in electron-density maps

Acta Crystallographica Section D: Biological Crystallography , Volume 66 (3): 285 – Feb 12, 2010

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 positions at spacings of approximately 0.6 A along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate C 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 A. 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 A for C 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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References (87)

Publisher
International Union of Crystallography
Copyright
Copyright (c) 2010 International Union of Crystallography
Subject
structure solution, model building, Protein Data Bank, chain tracing, PHENIX, experimental electron-density maps, Calpha positions
ISSN
0907-4449
eISSN
1399-0047
DOI
10.1107/S0907444910000272
pmid
20179340
Publisher site
See Article on Publisher Site

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 positions at spacings of approximately 0.6 A along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate C 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 A. 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 A for C atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality.

Journal

Acta Crystallographica Section D: Biological CrystallographyInternational Union of Crystallography

Published: Feb 12, 2010

Keywords: structure solution ; model building ; Protein Data Bank ; chain tracing ; PHENIX ; experimental electron-density maps ; C positions .

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