qize / sampl7

Challenge details, inputs, and (eventually) results for the SAMPL7 series of challenges

The SAMPL7 Blind Prediction Challenges for Computational Chemistry

Challenge details, inputs, and (eventually) results for the SAMPL7 series of challenges

See the SAMPL website for information on the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL) series of challenges as a whole. This repository focuses specifically on the SAMPL7 series of challenges.

Because these files are available publicly, we have no record of who downloads them. Therefore, you should sign up for notifications. Specifically, if you want to receive updates if we uncover any problems, it is imperative that you either (a) sign up for the SAMPL e-mail list via the D3R site, or (b) sign up for notifications of changes to this GitHub repository (the Watch button, above); ideally you would do both. Join our SAMPL7 e-mail list to get e-mails with SAMPL7-related announcements.

What's here

• Challenge Overview -- in progress
• Very preliminary information on the TrimerTrip host-guest challenge components in the host_guest directory.
• Final information on the Gibb octa acid-based challenge ("Gibb deep cavity cavitand" (GDCC) challenge) in the host_guest/GDCC_and_guests directory.
• Final information on the cyclodextrin derivatives challenge in the host_guest/cyclodextrin_derivatives directory and in our host-guest challenge description.
• Experimental details for the CD challenge in host_guest_description.md

You can consider the Gibb and Gilson challenges final and launched (though additional supporting files will be added, see below) and the Isaacs challenge will be finalized very soon.

What's coming

• Host-guest challenge information (late May 2019)
  • Finalized details on the Isaacs TrimerTrip challenge
  • Additional supporting files such as 3D structures of guests, additional structure files, and perhaps parameterized systems
  • Submission file formats

Changes and Data Set Versions

Release versions

Changes not in a release

• No formal releases yet

Challenge overview

(This section under construction)

Gibb Deep Cavity Cavitand (GDCC) binding of guests

One host-guest series is based on the Gibb Deep Cavity Cavitands (GDCCs), familiar from SAMPL4-6. However, this challenge we swap one of the hosts; previously, we used octa acid (OA) and tetramethyl octa acid (TEMOA); this challenge revisits OA but also utilizes a variant which changes the location of the carboxylates. Both were developed in the laboratory of Dr. Bruce Gibb (Tulane U), who will provide binding free energies and enthalpies, measured by ITC. In this case the challenge is to predict binding of eight compounds to exo-OA (a new host created and studied by the Gibb group and first disclosed in this challenge), and two of these to OA; the other six have been studied previously in OA. Existing benchmark datasets based on the OA host may be of interest for those preparing to tackle these new complexes: https://github.com/MobleyLab/benchmarksets; this perpetual review paper also provides a good introduction to the sampling and experimental issues which are known to be relevant in these systems. See the README on this challenge for more details.

Modified acyclic cucurbituril (TrimerTrip) binding of guests

The Isaacs lab is contributing data on binding of a series of guests to an acyclic cucubituril host, codenamed "TrimerTrip", as detailed in host_guest/Isaacs_clip tentatively. Guest selection is still being finalized to ensure good dynamic range, but it will likely include compounds which overlap with the GDCC and cyclodextrin-derivative challenges, with a total of roughly ten complexes being examined.

The cyclodextrin derivatives challenge

The Gilson lab is measuring binding of two guests to ten different hosts, comprising beta-cyclodextrin as well as nine different cyclodextrin derivatives which have a single functional group added at one location around the rim of the cavity. Binding is being characterized via ITC and NMR. The two guest compounds (R-rimantadine and trans-4-methylcyclohexanol) overlap with those used in the TrimerTrip and GDCC challenges. Full details are available.

LICENSE

This material here is made available under CC-BY and MIT licenses, as appropriate:

• MIT for all software/code
• CC-BY 4.0 for all other materials