Instructions around the Docking Results category

[mc-robinson]

Where to submit docking results to be uploaded to fragalysis and used for the triage of compounds.

Each person submitting results should create their own topic within this thread. Within that topic, the first post should roughly explain the rationale of the approach and provide a SDF file in the format described in Providing computed poses for others to look at

[reskyner]

Detailed instructions

1. Create a post on your own topic in this thread – the first post should roughly explain the rationale of the approach
2. Create the SDF file needed for upload to fragalysis. The specification can be found here: Providing computed poses for others to look at (I will update the specification in the comments thread of that post)
3. Make sure to add the link to your post from (1) to the ref_url field in the sdf file
4. Get an upload key from: https://fragalysis.diamond.ac.uk/viewer/cset_key/ (only need to do this the first time)
5. Validate and upload your sdf file: https://fragalysis.diamond.ac.uk/viewer/upload_cset/ and a zip file of pdb files if required.
6. The upload page will give you two links for compound set and protein set. Copy these links
7. Edit your original post adding the two links from above

[reskyner]

Example file that has been validated and uploaded to fragalysis: https://fragalysis.diamond.ac.uk/viewer/compound_set/AlessandroContini-NwatMM-GBSAcovalentrun1

Link to Jupyter notebook that generated the file: https://github.com/tdudgeon/jupyter_mpro/blob/master/contini/round1/sdf_prep.ipynb

[cole]

The upload page prompts you for a Target name. It would be good to provide guidance as to what is expected here.

[EKDavies]

I’m getting a SERVER ERROR (500) attempting to reach the URL https://fragalysis.diamond.ac.uk/viewer/upload_cset/ when trying to validate a docking set. Any ideas? Is it something I’m doing, not done etc