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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) sam...

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Autor principal: Terwilliger, Thomas C.
Formato: Texto
Lenguaje:English
Publicado: International Union of Crystallography 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2827349/
https://www.ncbi.nlm.nih.gov/pubmed/20179340
http://dx.doi.org/10.1107/S0907444910000272
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author Terwilliger, Thomas C.
author_facet Terwilliger, Thomas C.
author_sort Terwilliger, Thomas C.
collection PubMed
description 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.
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spelling pubmed-28273492010-02-24 Rapid chain tracing of polypeptide backbones in electron-density maps Terwilliger, Thomas C. Acta Crystallogr D Biol Crystallogr Research Papers 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. International Union of Crystallography 2010-03-01 2010-02-12 /pmc/articles/PMC2827349/ /pubmed/20179340 http://dx.doi.org/10.1107/S0907444910000272 Text en © Terwilliger 2010 http://creativecommons.org/licenses/by/2.0/uk/ 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.
spellingShingle Research Papers
Terwilliger, Thomas C.
Rapid chain tracing of polypeptide backbones in electron-density maps
title Rapid chain tracing of polypeptide backbones in electron-density maps
title_full Rapid chain tracing of polypeptide backbones in electron-density maps
title_fullStr Rapid chain tracing of polypeptide backbones in electron-density maps
title_full_unstemmed Rapid chain tracing of polypeptide backbones in electron-density maps
title_short Rapid chain tracing of polypeptide backbones in electron-density maps
title_sort rapid chain tracing of polypeptide backbones in electron-density maps
topic Research Papers
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2827349/
https://www.ncbi.nlm.nih.gov/pubmed/20179340
http://dx.doi.org/10.1107/S0907444910000272
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