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Title: Phaser.MRage: automated molecular replacement

The functionality of the molecular-replacement pipeline phaser.MRage is introduced and illustrated with examples. 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.
Authors:
 [1] ;  [2] ; ;  [1] ;  [2] ;  [1]
  1. University of Cambridge, CIMR, Wellcome Trust/MRC Building, Addenbrooke’s Hospital, Hills Road, Cambridge CB2 0XY (United Kingdom)
  2. Lawrence Berkeley National Laboratory, One Cyclotron Road, Mailstop 64R0121, Berkeley, CA 94720 (United States)
Publication Date:
OSTI Identifier:
22347840
Resource Type:
Journal Article
Resource Relation:
Journal Name: Acta Crystallographica. Section D: Biological Crystallography; Journal Volume: 69; Journal Issue: Pt 11; Other Information: PMCID: PMC3817702; PMID: 24189240; PUBLISHER-ID: ba5210; OAI: oai:pubmedcentral.nih.gov:3817702; Copyright (c) Bunkóczi et al. 2013; 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.; Country of input: International Atomic Energy Agency (IAEA)
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; LAYERS; MATHEMATICAL SOLUTIONS; MOLECULES; PROTEINS; SOLUTIONS