Fragment-based screening is now well-established as a powerful approach to early drug ("lead") discovery.
The user community is growing and you can follow current discussions in the XChem bulletin board.
For details of our fragment libraries, click here (or in left-hand menu).
The legendary Shifter is now commercially available from Oxford Lab Technologies. It is ridiculously cheap (seriously), fits on your favourite stereo microscope, and you can drive it with CSV files.
Those cool trays full of pins are available from Mitegen. They ought to simplify your life massively even if you're not doing fragment screening, watch the video on their page. Ask them for a quote for a tray pre-packed with barcoded pins in reusable bases: it's a lot less expensive than it sounds, and the investment will pay back for itself within an year.
SoakDB is a LIMS-in-a-box for the entire soaking and harvesting experiment. From here, the experiment is designed, the fragments are tracked, and the ouptut of the various programs and machines gathered into one place.
Software-wise it's primitive: an Excel interface to a sqlite database file. In practice, this has been a terrific solution: permissions are dealt with by the file-system, the db file can be emailed around, and some wicked VBA magic means the data persists only in the db file: Excel is essentially just the database UI.
One question is easy to answer: no, it's not a bells-and-whistles user interface; it's Excel. It is very powerful, but comes with no guarantees you'd know how to use it without training.
TeXRank (Ng et al, 2014, ActaD) is fully open source. If you want it deployed with your own imagers, it may take require a bit of work to get everything integrated - it's doable but a lot of faff, so if you have money but no time, contact Frank von Delft who can put you in touch with someone that can help.
This software connects to a camera, and if it sees you're holding a puck full pins in the field of view, it will read all the barcodes and dump them to clipboard as a lst of 16 numbers (blanks for empty pins).
Sounds easy, was hard...
Executables can be downloaded from GitHib, here.
3D print files for the stand can be downloaded here.
Some instructions can be found here.
We recommend using it with this camera (£80 on Amazon) or any camera with manual focus. Detailed setup instructions to follow, though there are no tricks.
XChemExplorer (XCE) is the counterpart to SoakDB on the data analysis side. It manages large-scale processing and analysis of the data that gushes off the beamline, 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 your structures using ccp4 or phenix interfaces.
You can read the XCE brief manual and check for ongoing upgrades and submit issues and suggestions to github.
XCE will be available for download soon, though with no guarantees of software support; be sure to subscribe to XCHEMBB. If you have the latest CCP4 installed, this will at least launch on your machine, though making it actually work on non-Diamond systems might be a different matter: possible, and we'd be happy to help, but out of our own scope.
PanDDA was developed by Nicholas Pearce to find and extract weak density from large numbers of datasets. The software will soon be available in CCP4, but can currently be obtained by subscribing to the XCHEMBB mailing list and looking in the archives on July 19th, 2016.
The manuscript has been submitted, meanwhile you can read it on bioRXiv.
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