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Phaser.MRage: automated molecular replacement.

Published version
Peer-reviewed

Type

Article

Change log

Authors

Bunkóczi, Gábor 
Echols, Nathaniel 
McCoy, Airlie J 
Oeffner, Robert D 
Adams, Paul D 

Abstract

Phaser.MRage is a molecular-replacement automation framework that implements a full model-generation workflow and provides several layers of model exploration to the user. It is designed to handle a large number of models and can distribute calculations efficiently onto parallel hardware. In addition, phaser.MRage can identify correct solutions and use this information to accelerate the search. Firstly, it can quickly score all alternative models of a component once a correct solution has been found. Secondly, it can perform extensive analysis of identified solutions to find protein assemblies and can employ assembled models for subsequent searches. Thirdly, it is able to use a priori assembly information (derived from, for example, homologues) to speculatively place and score molecules, thereby customizing the search procedure to a certain class of protein molecule (for example, antibodies) and incorporating additional biological information into molecular replacement.

Description

Keywords

automation, molecular replacement, phaser.MRage, pipeline, Amino Acid Substitution, Artificial Intelligence, Computational Biology, Crystallography, X-Ray, Databases, Protein, Models, Molecular, Protein Multimerization, Protein Structure, Tertiary, Software

Journal Title

Acta Crystallogr D Biol Crystallogr

Conference Name

Journal ISSN

0907-4449
1399-0047

Volume Title

69

Publisher

International Union of Crystallography (IUCr)

Rights

All rights reserved
Sponsorship
Wellcome Trust (100140/Z/12/Z)
Wellcome Trust (082961/Z/07/Z)
National Institute of General Medical Sciences (P01GM063210)