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How far are we from automatic crystal structure solution via molecular-replacement techniques?
Although the success of molecular-replacement techniques requires the solution of a six-dimensional problem, this is often subdivided into two three-dimensional problems. REMO09 is one of the programs which have adopted this approach. It has been revisited in the light of a new probabilistic approac...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
International Union of Crystallography
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939436/ https://www.ncbi.nlm.nih.gov/pubmed/31909739 http://dx.doi.org/10.1107/S2059798319015468 |
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author | Burla, Maria Cristina Carrozzini, Benedetta Cascarano, Giovanni Luca Giacovazzo, Carmelo Polidori, Giampiero |
author_facet | Burla, Maria Cristina Carrozzini, Benedetta Cascarano, Giovanni Luca Giacovazzo, Carmelo Polidori, Giampiero |
author_sort | Burla, Maria Cristina |
collection | PubMed |
description | Although the success of molecular-replacement techniques requires the solution of a six-dimensional problem, this is often subdivided into two three-dimensional problems. REMO09 is one of the programs which have adopted this approach. It has been revisited in the light of a new probabilistic approach which is able to directly derive conditional distribution functions without passing through a previous calculation of the joint probability distributions. The conditional distributions take into account various types of prior information: in the rotation step the prior information may concern a non-oriented model molecule alone or together with one or more located model molecules. The formulae thus obtained are used to derive figures of merit for recognizing the correct orientation in the rotation step and the correct location in the translation step. The phases obtained by this new version of REMO09 are used as a starting point for a pipeline which in its first step extends and refines the molecular-replacement phases, and in its second step creates the final electron-density map which is automatically interpreted by CAB, an automatic model-building program for proteins and DNA/RNA structures. |
format | Online Article Text |
id | pubmed-6939436 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | International Union of Crystallography |
record_format | MEDLINE/PubMed |
spelling | pubmed-69394362020-01-06 How far are we from automatic crystal structure solution via molecular-replacement techniques? Burla, Maria Cristina Carrozzini, Benedetta Cascarano, Giovanni Luca Giacovazzo, Carmelo Polidori, Giampiero Acta Crystallogr D Struct Biol Ccp4 Although the success of molecular-replacement techniques requires the solution of a six-dimensional problem, this is often subdivided into two three-dimensional problems. REMO09 is one of the programs which have adopted this approach. It has been revisited in the light of a new probabilistic approach which is able to directly derive conditional distribution functions without passing through a previous calculation of the joint probability distributions. The conditional distributions take into account various types of prior information: in the rotation step the prior information may concern a non-oriented model molecule alone or together with one or more located model molecules. The formulae thus obtained are used to derive figures of merit for recognizing the correct orientation in the rotation step and the correct location in the translation step. The phases obtained by this new version of REMO09 are used as a starting point for a pipeline which in its first step extends and refines the molecular-replacement phases, and in its second step creates the final electron-density map which is automatically interpreted by CAB, an automatic model-building program for proteins and DNA/RNA structures. International Union of Crystallography 2020-01-01 /pmc/articles/PMC6939436/ /pubmed/31909739 http://dx.doi.org/10.1107/S2059798319015468 Text en © Burla et al. 2020 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Ccp4 Burla, Maria Cristina Carrozzini, Benedetta Cascarano, Giovanni Luca Giacovazzo, Carmelo Polidori, Giampiero How far are we from automatic crystal structure solution via molecular-replacement techniques? |
title | How far are we from automatic crystal structure solution via molecular-replacement techniques? |
title_full | How far are we from automatic crystal structure solution via molecular-replacement techniques? |
title_fullStr | How far are we from automatic crystal structure solution via molecular-replacement techniques? |
title_full_unstemmed | How far are we from automatic crystal structure solution via molecular-replacement techniques? |
title_short | How far are we from automatic crystal structure solution via molecular-replacement techniques? |
title_sort | how far are we from automatic crystal structure solution via molecular-replacement techniques? |
topic | Ccp4 |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939436/ https://www.ncbi.nlm.nih.gov/pubmed/31909739 http://dx.doi.org/10.1107/S2059798319015468 |
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