Data Analysis and Collaboration Tools

XChemExplorer (XCE) manages large-scale processing and analysis of X-ray diffraction data, provides an interface to PanDDA, and guides the validation workflow for PanDDA-derived models. It is enormously powerful, and an eye-opener if you've been trying to get through a large number of structures using CCP4 or Phenix interfaces.

XCE can be downloaded directly from github, but support with local deployment is not available from the XChem team.

PanDDA was developed by Nicholas Pearce to find and extract weak density from large numbers of datasets.  The software is distributed with CCP4, and detailed instructions can be found here.

An updated version of PanDDA (PanDDA 2) has been developed by Conor Wild and differs from PanDDA in two major methodological ways.

Firstly, it attempts to identify which sets of datasets should be used to produce a statistical model which has the optimal contrast (to each test dataset individually). This allows it to handle subtle heterogeneity between datasets.

Secondly it attempts to autobuild the events returned, and then rank the events based on the quality of the model of the fragment that could be constructed. This allows improved rankings of events.

PanDDA2 is distributed on GitHub.

Pearce, N., Krojer, T., Bradley, A. et al. A multi-crystal method for extracting obscured crystallographic states from conventionally uninterpretable electron density. Nat Commun 8, 15123 (2017). https://doi.org/10.1038/ncomms15123

We have been building a Cloud-based platform where your XChem hits can both be publicised, but also analysed for progressing to potency.  Thus, all the screens performed by the SGC, which are made fully public immediately, are served on Fraglaysis, and help demonstrate a new paradigm of serving structural ligand-binding data.  Users are free to volunteer their data too.

Fragalysis also enables picking and calculating compounds with approximately cutting-edge computational tools, which we try to make as simple to access as possible to use.  Thanks to a big investment from Janssen via the IMI-funded ULTRA-DD project, Fragalysis is now quickly turning from prototype into useful thing.

Fragalysis itself:  fragalysis.diamond.ac.uk

Background, descriptions and development priorities at the fragalysis wiki