title: Phaser.MRage: automated molecular replacement.
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.
authors.affiliation: Department of Haematology, University of Cambridge, CIMR, Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0XY, England.
authors.forename: Gábor
authors.initials: G
authors.lastname: Bunkóczi
authors.forename: Nathaniel
authors.initials: N
authors.lastname: Echols
authors.forename: Airlie J
authors.initials: AJ
authors.lastname: McCoy
authors.forename: Robert D
authors.initials: RD
authors.lastname: Oeffner
authors.forename: Paul D
authors.initials: PD
authors.lastname: Adams
authors.forename: Randy J
authors.initials: RJ
authors.lastname: Read
mesh_terms: D019943:Amino Acid Substitution; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray / Q000379:methods / Q000639:trends; D030562:Databases, Protein / Q000592:standards; D008958:Models, Molecular; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D012984:Software
keywords: automation; molecular replacement; phaser.MRage; pipeline