Closed since over 2 years ago
Intermediate Overall Small Molecule DesignThis puzzle is a followup to the SARS-CoV-2 Nsp3 macrodomain design challenges. Help us rank potential active compounds!
Phase 2 of the CACHE challenge #3 is a ranking of all 1739 molecules which the various participants submitted for testing. In this puzzle you don't have free design with the Small Molecule Design tool, but you instead have the Ligand Queue which will provide you with a small number of possible compounds. You can then use the compound library panel to find related compounds specifically from the library of tested compounds. Then attempt to find the best binding position for the compounds.
Note: To get the most out of the small molecule design tools, we recommend changing you view settings to the Small Molecule Design Preset.
For this round, the ligand queue has a different set of possible compounds (these may get reordered to promote balanced sampling). In addition, we've turned on the Compound Library objective, which should make sure that compounds we're interested in make it to the top of the ranking. - Remember that you may need to submit Ligand Queue compounds to the Compound Library, wait for the results, and then hit wiggle on the compound before the Compound Library objective recognizes the compound. Bounce back and forth between the ligand queue and the compound library search to seek out compounds you think bind best.
Participation in CACHE puzzles is subject to the CACHE Terms of Participation, in particular “the Challenge IP [including Challenge Compounds] will be made freely available in the public domain pursuant to Creative Commons Attribution Only (CC-BY 4.0 or subsequent versions) licensing terms, with the intent that such Challenge IP may be Used and practiced by Users for any purpose”.
100 pts.
19,988
Does this mean that if a library previously contained 35 compounds, it will still contain 35 compounds, but some of them may have different similarity scores from before? Does this mean that if a library previously contained 35 compounds, it might now contain 36 or more compounds?
I think the results of submitting the same compound for the search will be mostly the same, but it may have some differences in which compounds and how many are returned.
Thank you, @rmoretti, for your continued efforts to improve our tools.
Unfortunately, it seems that the Compound Library is unresponsive at the moment (Monday 09 October 2023 around 20:00h UTC). And in Saturday's version of the Library for the initial compound, Entry 7 still shows Similarity 1.000000 to itself, instead of an Exact Match. Hence: no bonus for this one.
Hope this will change once the new Library results come through.
@HuubR We're having some disk issues with the system which runs the compound library search. It theoretically shouldn't have cause things to go down, but apparently there's been some knock-on effects. Things should (hopefully) be back up sometime today.
Although I tried, I didn't explore as much with this puzzle as I wanted. If possible, please either extend the deadline for this puzzle by a week, or make a sequel to this puzzle that lets us load results from both puzzles 2360 and 2363 as if they had scores consistent with the latest, most correct versions of the Compound Library and Ligand Queue.
Thanks!
