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The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline

A description of REMO22, a new molecular replacement program for proteins and nucleic acids, is provided. This program, as with REMO09, can use various types of prior information through appropriate conditional distribution functions. Its efficacy in model searching has been validated through severa...

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Autores principales: Carrozzini, Benedetta, Cascarano, Giovanni Luca, Giacovazzo, Carmelo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10094557/
https://www.ncbi.nlm.nih.gov/pubmed/37047043
http://dx.doi.org/10.3390/ijms24076070
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author Carrozzini, Benedetta
Cascarano, Giovanni Luca
Giacovazzo, Carmelo
author_facet Carrozzini, Benedetta
Cascarano, Giovanni Luca
Giacovazzo, Carmelo
author_sort Carrozzini, Benedetta
collection PubMed
description A description of REMO22, a new molecular replacement program for proteins and nucleic acids, is provided. This program, as with REMO09, can use various types of prior information through appropriate conditional distribution functions. Its efficacy in model searching has been validated through several test cases involving proteins and nucleic acids. Although REMO22 can be configured with different protocols according to user directives, it has been developed primarily as an automated tool for determining the crystal structures of macromolecules. To evaluate REMO22’s utility in the current crystallographic environment, its experimental results must be compared favorably with those of the most widely used Molecular Replacement (MR) programs. To accomplish this, we chose two leading tools in the field, PHASER and MOLREP. REMO22, along with MOLREP and PHASER, were included in pipelines that contain two additional steps: phase refinement (SYNERGY) and automated model building (CAB). To evaluate the effectiveness of REMO22, SYNERGY and CAB, we conducted experimental tests on numerous macromolecular structures. The results indicate that REMO22, along with its pipeline REMO22 + SYNERGY + CAB, presents a viable alternative to currently used phasing tools.
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spelling pubmed-100945572023-04-13 The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline Carrozzini, Benedetta Cascarano, Giovanni Luca Giacovazzo, Carmelo Int J Mol Sci Article A description of REMO22, a new molecular replacement program for proteins and nucleic acids, is provided. This program, as with REMO09, can use various types of prior information through appropriate conditional distribution functions. Its efficacy in model searching has been validated through several test cases involving proteins and nucleic acids. Although REMO22 can be configured with different protocols according to user directives, it has been developed primarily as an automated tool for determining the crystal structures of macromolecules. To evaluate REMO22’s utility in the current crystallographic environment, its experimental results must be compared favorably with those of the most widely used Molecular Replacement (MR) programs. To accomplish this, we chose two leading tools in the field, PHASER and MOLREP. REMO22, along with MOLREP and PHASER, were included in pipelines that contain two additional steps: phase refinement (SYNERGY) and automated model building (CAB). To evaluate the effectiveness of REMO22, SYNERGY and CAB, we conducted experimental tests on numerous macromolecular structures. The results indicate that REMO22, along with its pipeline REMO22 + SYNERGY + CAB, presents a viable alternative to currently used phasing tools. MDPI 2023-03-23 /pmc/articles/PMC10094557/ /pubmed/37047043 http://dx.doi.org/10.3390/ijms24076070 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Carrozzini, Benedetta
Cascarano, Giovanni Luca
Giacovazzo, Carmelo
The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline
title The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline
title_full The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline
title_fullStr The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline
title_full_unstemmed The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline
title_short The Automatic Solution of Macromolecular Crystal Structures via Molecular Replacement Techniques: REMO22 and Its Pipeline
title_sort automatic solution of macromolecular crystal structures via molecular replacement techniques: remo22 and its pipeline
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10094557/
https://www.ncbi.nlm.nih.gov/pubmed/37047043
http://dx.doi.org/10.3390/ijms24076070
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