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GC3 Stage 2 Answers Posted

Answers are now available for all kinase and cathepsin Stage 2 components. To get them, please log in to the D3R site and navigate to the Data Download tab for each subchallenge.

Note that the D3R workshop discount for lodging at the La Jolla Shores hotel expires January 19 -- about a week from now. The hotel is walking distance to the workshop, which will be held at the Scripps Institution of Oceanography. We hope to see you in February!

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Grand Challenge 3 Update

The D3R website is now open for GC3 Stage 2 submissions. Instructions, templates, and example files are now posted here (https://drugdesigndata.org/about/grand-challenge-3) , for both Cathepsin S and all the kinase subchallenges.

The deadline for the kinase predictions remains 11:59pm Pacific Time, December 1, but we have extended the deadline for Cathepsin S predictions to 11:59pm Pacific Time, December 15, because of the addition of Stage 1b.

We are excited to announce that registration is now open for the 2018 D3R workshop, to be held Feb 21-23, at UC San Diego's Scripps Institution of Oceanography. Feb 21 will include only an evening reception, and Feb 22-23 will be full meeting days. We look forward to seeing you in sunny La Jolla, California!

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GC3 Stage 1b

Dear GC3 Participant,

We have discovered an error in our preparation of the “example” files we provided on 9/21 for the pose-prediction challenge. The example files are fine for their purpose, but we inadvertently populated them with the protein structures from the actual crystallographic results for the corresponding ligands. As a consequence, if a participant, for some reason, chose to dock into these structures, he or she would have been doing self-docking calculations, rather than cross-docking calculations. We cannot know for sure whether anyone used the example protein structures in their calculations, so this component of the challenge can no longer be viewed as an entirely rigorous comparison of methods. On the other hand, we have no reason to expect anyone would have used these files for docking, and we believe that the results can still be useful and informative, both for the individual submitter and for the larger community. Our thought, therefore, is to go ahead with the normal evaluation of all stage 1 predictions, but to be clear in reporting the results that they can no longer be viewed as rigorously comparable.

So that Grand Challenge 3 will include a pose-prediction challenge whose results can be compared without qualification, we are adding a Stage 1b challenge, in which participants are invited to do self-docking calculations into the protein structures from the true co-crystal structures. This stage is of scientific interest, as it allows docking methodologies to be compared without the complicating factor of protein structure selection.

Stage 1b will open Monday, October 9. The data package for Stage 1b, comprising the protein structures for self-docking, will be available here (https://drugdesigndata.org/about/grand-challenge-3/cathepsin_s#data-download) . We propose a deadline of 11:59 pm, Pacific Time, October 23.

We apologize for the mistake and invite you to reply with any thoughts or suggestions.

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GC3 Stage 1 Update

We have several important announcements regarding this challenge:

  • Our rerefinement of the Cathepsin S crystal structures revealed that three ligands for which the SMILES strings we were given listed a trimethyl group actually have a trifluoro group. We confirmed this correction with Janssen. The compounds are CatS_7, Cat_9, and CatS_14. A revised Stage 1 data package is available here (https://drugdesigndata.org/about/grand-challenge-3/cathepsin_s#data-download) .
  • Because of this correction, Stage 1 is being extended to 5:00 pm Pacific Time, October 3.
  • Submission instructions are now available here (https://drugdesigndata.org/about/grand-challenge-3-submission-instructions-cathepsin-stage1) .
  • The website will open for submissions on September 25. We recommend submitting your predictions in advance of the deadline, so you will have sufficient time to correct any problems identified by our validation software.
Happy docking! D3R Team

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GC3 Open Today

Dear Colleague,We are excited to announce today's opening of D3R's Grand Challenge 3!The Stage 1 pose prediction component ends October 1, and the full challenge closes December 1.Full information, registration, and data package downloads, are available at https://drugdesigndata.org/about/grand-challenge-3 Happy docking D3R Team

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SAMPL6 host-guest challenge is now open

We are excited to announce that the SAMPL6 host-guest challenge is now open!

Details and a link to the data package are available at the D3R SAMPL6 page. Note that, unlike in prior challenges, the data package is now being provided via GitHub. This is because the D3R site is being updated, and also to facilitate revision control. If you want to join SAMPL6, please sign up on not only the D3R site, but also the GitHub site (“watch” the repository), to make sure you receive all relevant notifications.

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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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