D3R Blog

GC2 Participant Updates

• 02:27pm April 24, 2017
• 1723 views
• gc2

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

• 02:20pm April 24, 2017
• 1551 views
• d3r, gc2, pl-2016-1

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

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D3R Webinar - March 27, 2017

• 11:00am March 22, 2017
• 1265 views
• gc2, pl-2016-1

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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GC2 Protocols and PL2016-1

• 02:19pm March 14, 2017
• 1226 views
• gc2, pl-2016-1

More updates, and an invitation!

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GC2 Protocols, Papers, Etc

• 02:18pm March 14, 2017
• 1356 views
• gc2

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

• 12:43pm February 23, 2017
• 1236 views
• gc2

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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D3R Grand Challenge 2: Stage 2 Closing and Answers

• 02:20pm February 16, 2017
• 1248 views
• gc2

We are happy to report that there were 124 submissions from 33 participants for Stage 2 of Grand Challenge 2! The answer file of measured IC50 values is available here (direct download here).
Pat Walters has generously agreed to lead the evaluation process again.  Evaluation results will be made available as they become available.  
We will also be sending more information about the March 27 Webinar to discuss this challenge and the PL-2016-1 mini-challenge. We hope to interact with you there!

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D3R Grand Challenge 2: Dealing with 5-character PDB IDs

• 03:17pm January 31, 2017
• 1214 views
• gc2

Several participants have asked how to make acceptable four-character PDB and MOL file names from the 5-character PDB IDs provided at the close of Stage 1.
To do this, just leave the "1" off the beginning of the name. For example, 1HGAF.pdb would become HGAF.pdb, leading to file names like HGAF-FXR_1.mol and HGAF-FXR_1.pdb.

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D3R Grand Challenge 2: Extension of Stage 2 and Stage 1 Pose Evaluations

• 02:35pm January 25, 2017
• 1203 views
• gc2

1. In response to a participant request, and in light of the late release of corrected Stage 1 cocrystal structures, the deadline for Stage 2 predictions is extended by one week, to February 8.
2. Summary evaluations of your Stage 1 pose predictions are available here. Look for your results by Receipt ID.As you could submit up to five poses for each ligand, we list Mean RMSD of Top Scoring Pose (the mean, across all ligands, of the poses you listed as the top scoring ones) and Mean RMSD of Lowest RMSD Poses (the mean, across all ligands, of the lowest RMSD poses of the five for each ligand). The RMSDs were computed by aligning your predictions against the new, re-refined crystal structures, using binding-site atoms to do the superpositions. Ligand-by-ligand statistics will appear on the D3R website soon.

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D3R Grand Challenge 2: Crystallographic mtz files now available

• 03:12pm January 20, 2017
• 1184 views
• gc2

In case you would like to investigate the Stage 1 crystal structures in more detail, we have posted the mtz files here. (Note that this is a 99MB download.)

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