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Phasertng: directed acyclic graphs for crystallographic phasing.

Authors
  • McCoy, Airlie J1
  • Stockwell, Duncan H1
  • Sammito, Massimo D1
  • Oeffner, Robert D1
  • Hatti, Kaushik S1
  • Croll, Tristan I1
  • Read, Randy J1
  • 1 Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2 0XY, United Kingdom. , (United Kingdom)
Type
Published Article
Journal
Acta crystallographica. Section D, Structural biology
Publication Date
Jan 01, 2021
Volume
77
Issue
Pt 1
Pages
1–10
Identifiers
DOI: 10.1107/S2059798320014746
PMID: 33404520
Source
Medline
Keywords
Language
English
License
Unknown

Abstract

Crystallographic phasing strategies increasingly require the exploration and ranking of many hypotheses about the number, types and positions of atoms, molecules and/or molecular fragments in the unit cell, each with only a small chance of being correct. Accelerating this move has been improvements in phasing methods, which are now able to extract phase information from the placement of very small fragments of structure, from weak experimental phasing signal or from combinations of molecular replacement and experimental phasing information. Describing phasing in terms of a directed acyclic graph allows graph-management software to track and manage the path to structure solution. The crystallographic software supporting the graph data structure must be strictly modular so that nodes in the graph are efficiently generated by the encapsulated functionality. To this end, the development of new software, Phasertng, which uses directed acyclic graphs natively for input/output, has been initiated. In Phasertng, the codebase of Phaser has been rebuilt, with an emphasis on modularity, on scripting, on speed and on continuing algorithm development. As a first application of phasertng, its advantages are demonstrated in the context of phasertng.xtricorder, a tool to analyse and triage merged data in preparation for molecular replacement or experimental phasing. The description of the phasing strategy with directed acyclic graphs is a generalization that extends beyond the functionality of Phasertng, as it can incorporate results from bioinformatics and other crystallographic tools, and will facilitate multifaceted search strategies, dynamic ranking of alternative search pathways and the exploitation of machine learning to further improve phasing strategies. open access.

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