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D3R Grand Challenge 3 Opening Soon!

Dear Colleague, We are pleased to announce that Grand Challenge 3 (GC3) is planned to open at the start of September, with the first stage closing ~September 25, the second stage closing at the star...

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SAMPL Survey

As you may know, the SAMPL series of blinded prediction challenges focuses on relatively simple, but still difficult, challenges, such as the prediction of hydration free energies, distribution coefficients, host-guest binding affinities, and affinities of small molecules for model binding sites in proteins. SAMPL thus complements D3R, which focus on systems of direct pharmaceutical interest.

Organizers of SAMPL are now developing plans for future challenges and seeking funding to support them. Your input is invited via a brief survey, which is accompanied by a draft roadmap of activities over the next ~5 years.

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GC2 Participant Updates

  1. Per a participant request, we have provided detailed listings of pose RMSDs across all submissions. See Pose Predictions - Details here, or use this direct link.
  2. The error statistics we initially provided for Scores and Free Energies did not properly account for the experimental uncertainties of the IC50 data. We have corrected this and posted new statistics here. The original file are still provided for your reference, but are now marked as obsolete. Fortunately, there is little change in the results.
  3. Note that the deadline for receipt of your articles for the special issue of JCAMD is June 1. Submission instructions are posted here, under Special Journal Issues.
  4. Please send us a separate email when you submit your article, so we can be sure it gets connected with the special issue.

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Webinar Presentations Available

Slides and videos for presentations from the March 27 D3R Webinar are now available here.

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D3R at ACS San Francisco

You are invited to meet with D3R team-members Rommie Amaro, Shuai Liu, Zied Gaieb, and Jeff Wagner at the San Francisco ACS National Meeting this April! D3R will be at the COMP poster session ( 6-8pm, Tuesday, April 4) and look forward to chatting with participants, data contributors, and others.

Jeff will present a poster about CELPP (COMP #411), and Shuai speak about CELPP at 9:30 am, Wed April 5, at the Park Center Hotel (CINF #140).

We look forward to seeing you!

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D3R Webinar - March 27, 2017

We are pleased to invite you to join the D3R Webinar, 8am - 2pm Pacific Time, Monday, March 27. The agenda is here; topics include: reports on the PL-2016-1 and GC2 challenges refinement of co-crystal structures plans for future Grand Challenges and CELPP Please pre-register via this link. You will then be sent a confirmation email. Please follow the "check system requirements" link in that email, to make sure you have the required plugin and are ready to go before the meeting starts.

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PL-2016-1 articles and videos

Important announcements -- with apologies for cross-postings to GC2 participants!

D3R Webinar, March 27
Send Us a Video Seminar about your PL-2016-1 Results!
Special Issue of JCAMD
Release of Protocols and Predictions

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GC2 Protocols and PL2016-1

More updates, and an invitation!

Sharing of GC2 Protocols
Sharing of GC2 Predictions and Evaluation Scripts
Send Us a Video Seminar about your GC2 Results!

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GC2 Protocols, Papers, Etc

We have a number of updates and questions for you this week!  Sharing of GC2 Protocols Some participants have asked for information on other participants' computational protocols, and we plan to share these, coded by submission IDs, on the D3R website. If you are participating anonymously and are concerned that your protocol will de-anonymize you, please let us know as soon as possible. Special Issue of JCAMD for your GC2 paper You are invited to submit a paper about your GC2 calculations to another special issue of the Journal of Computer-Aided Molecular Design. (Thanks to editor Terry Stouch!). We anticipate a submission deadline of June 1, 2017. Instructions for submitting your article are provided here. Citable DOIs for Datasets Digital Object Identifiers (DOIs) have been created for the Grand Challenge 2015 datasets and are available on the Datasets page.  We are working on DOIs for the GC2 datasets and hope to have them available in time to be cited in your in your JCAMD paper. Grand Challenge 2 Webinar, March 27 We plan to invite a number of participants to present their experiences with GC2 and PL-2016-1 at the webinar, with time for Q/A. There will also be talks by Stephen Burley about Xray structures of protein-ligand cocrystal structures, and by the experimentalists who generated the challenge data. The preliminary agenda is posted here.

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D3R Grand Challenge 2: Prediction Evaluations Available

We have completed initial processing of all Stage 1 and Stage 2 predictions, and have posted them on the D3R website. To access them, please go to this page, log in, and click the link under Evaluation Results at the top right.
This will take you to a page with downloadable CSV files and web-based graphical analyses that put your predictions into the context of others. You can find your own results by its submission ID.
The page also summarizes how the statistics were computed and how compounds measured as racemates were dealt with in the evaluations. The information on racemates is also provided in this document. 

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