BALBES : a molecular-replacement pipeline

Abstract

The number of macromolecular structures solved and deposited in the Protein Data Bank (PDB) is higher than 40 000. Using this information in macromolecular crystallography (MX) should in principle increase the efficiency of MX structure solution. This paper describes a molecular-replacement pipeline, BALBES, that makes extensive use of this repository. It uses a reorganized database taken from the PDB with multimeric as well as domain organization. A system manager written in Python controls the workflow of the process. Testing the current version of the pipeline using entries from the PDB has shown that this approach has huge potential and that around 75% of structures can be solved automatically without user intervention.

Cited by papers we hold 13

• The CCP 4 suite: integrative software for macromolecular crystallography · 2023
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• Structure of MlaFB uncovers novel mechanisms of ABC transporter regulation · 2020
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• Mechanism of synergistic actin filament pointed end depolymerization by cyclase-associated protein and cofilin · 2019
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• Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions · 2015
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• Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation · 2015
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• The PDB_REDO server for macromolecular structure model optimization · 2014
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• Phaser.MRage : automated molecular replacement · 2013
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• OTU Deubiquitinases Reveal Mechanisms of Linkage Specificity and Enable Ubiquitin Chain Restriction Analysis · 2013
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• phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta · 2012
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• Low-resolution refinement tools in REFMAC 5 · 2012
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• Improvement of molecular-replacement models with Sculptor · 2011
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• Overview of the CCP 4 suite and current developments · 2011
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