title: The XChemExplorer graphical workflow tool for routine or large-scale protein-ligand structure determination.
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), Acta Cryst. D67, 235-242] or PHENIX [Adams et al. (2010), 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.
authors.affiliation: Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England.
authors.forename: Tobias
authors.initials: T
authors.lastname: Krojer
authors.affiliation: Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England.
authors.forename: Romain
authors.initials: R
authors.lastname: Talon
authors.affiliation: Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England.
authors.forename: Nicholas
authors.initials: N
authors.lastname: Pearce
authors.affiliation: Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England.
authors.forename: Patrick
authors.initials: P
authors.lastname: Collins
authors.affiliation: Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England.
authors.forename: Alice
authors.initials: A
authors.lastname: Douangamath
authors.affiliation: Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England.
authors.forename: Jose
authors.initials: J
authors.lastname: Brandao-Neto
authors.affiliation: Diamond Light Source Ltd, Harwell Science and Innovation Campus, Didcot OX11 0QX, England.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Dias
authors.affiliation: Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England.
authors.forename: Brian
authors.initials: B
authors.lastname: Marsden
authors.affiliation: Structural Genomics Consortium, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, England.
authors.forename: Frank
authors.initials: F
authors.lastname: von Delft
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D018360:Crystallography, X-Ray; D008024:Ligands; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface; D057188:Workflow
chemical_list: D008024:Ligands; D011506:Proteins
keywords: PanDDA; XChemExplorer; fragment screening; protein–ligand structure; structure-based ligand design