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The XChemExplorer graphical workflow tool for routine or large-scale protein–ligand structure determination

DOI: 10.1107/S2059798316020234 DOI Help

Authors: Tobias Krojer (Structural Genomics Consortium, University of Oxford) , Romain Talon (Structural Genomics Consortium, University of Oxford) , Nicholas Pearce (Structural Genomics Consortium, University of Oxford) , Patrick Collins (Diamond Light Source) , Alice Douangamath (Diamond Light Source) , Jose Brandao-neto (Diamond Light Source) , Alexandre Dias (Diamond Light Source) , Brian Marsden (Structural Genomics Consortium, University of Oxford) , Frank Von Delft (Structural Genomics Consortium, Uiversity of Oxford; Diamond Light Source; University of Johannesburg)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Acta Crystallographica Section D Structural Biology , VOL 73

State: Published (Approved)
Published: March 2017

Open Access Open Access

Abstract: XChemExplorer (XCE) is a data-management and workflow tool to support large-scale simultaneous analysis of protein–ligand complexes during structure-based ligand discovery (SBLD). The user interfaces of established crystallo­graphic software packages such as CCP4 [Winn et al. (2011[Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.]), Acta Cryst. D67, 235–242] or PHENIX [Adams et al. (2010[Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.]), Acta Cryst. D66, 213–221] have entrenched the paradigm that a `project' is concerned with solving one structure. This does not hold for SBLD, where many almost identical structures need to be solved and analysed quickly in one batch of work. Functionality to track progress and annotate structures is essential. XCE provides an intuitive graphical user interface which guides the user from data processing, initial map calculation, ligand identification and refinement up until data dissemination. It provides multiple entry points depending on the need of each project, enables batch processing of multiple data sets and records metadata, progress and annotations in an SQLite database. XCE is freely available and works on any Linux and Mac OS X system, and the only dependency is to have the latest version of CCP4 installed. The design and usage of this tool are described here, and its usefulness is demonstrated in the context of fragment-screening campaigns at the Diamond Light Source. It is routinely used to analyse projects comprising 1000 data sets or more, and therefore scales well to even very large ligand-design projects.

Journal Keywords: XChemExplorer; PanDDA; structure-based ligand design; protein–ligand structure; fragment screening

Subject Areas: Information and Communication Technology, Biology and Bio-materials, Chemistry


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Added On: 28/02/2017 09:35

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