Open AccessEvaluating the solution from MrBUMP and BALBES
Author(s) -
Keegan Ronan M.,
Long Fei,
Fazio Vincent J.,
Winn Martyn D.,
Murshudov Garib N.,
Vagin Alexei A.
Publication year - 2011
Publication title -
acta crystallographica section d
Language(s) - English
Resource type - Journals
ISSN - 1399-0047
DOI - 10.1107/s0907444911007530
Subject(s) - molecular replacement , computer science , software , set (abstract data type) , sequence (biology) , process (computing) , data mining , key (lock) , scale (ratio) , information retrieval , theoretical computer science , algorithm , programming language , protein structure , biology , geography , cartography , biochemistry , genetics , computer security
Molecular replacement is one of the key methods used to solve the problem of determining the phases of structure factors in protein structure solution from X‐ray image diffraction data. Its success rate has been steadily improving with the development of improved software methods and the increasing number of structures available in the PDB for use as search models. Despite this, in cases where there is low sequence identity between the target‐structure sequence and that of its set of possible homologues it can be a difficult and time‐consuming chore to isolate and prepare the best search model for molecular replacement. MrBUMP and BALBES are two recent developments from CCP 4 that have been designed to automate and speed up the process of determining and preparing the best search models and putting them through molecular replacement. Their intention is to provide the user with a broad set of results using many search models and to highlight the best of these for further processing. An overview of both programs is presented along with a description of how best to use them, citing case studies and the results of large‐scale testing of the software.