Leaving Community
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
D3R Grand Challenge 2: Free Energy Predictions
- 05:01pm January 18, 2017
- 1264 views
- gc2
A participant has asked for a way of submitting predictions for just a subset of the ligands in a free energy set.
To do this, please write "NoPred" (case-insensitive) in the
FreeEnergies.csv file, in place of the computed affinity for the ligand
in question. You can leave the corresponding uncertainty value blank.
Note, however, that a submission that is missing predictions for some
ligands will not necessarily be evaluated together with the complete
submissions.
Rerefined Cocrystal Structures: Default and Tight
- 01:29pm January 17, 2017
- 1115 views
- gc2
Corrected crystal structures are now available on the Grand Challenge 2 page. We apologize that this has taken so long. A summary of the issues we encountered when making the corrections is provided below, and Dr. Stephen Burley, D3R's crystallography lead, and director of the RCSB PDB, will discuss these further at the March 27 Webinar. We are rerunning the RMSD calculations, but preliminary calculations indicate that using the corrected structures changes the pose RMSDs by at most ~0.1 Angstrom. Additionally, instructions for your Stage 2 submissions are now available via the Grand Challenge 2 page or directly here. The D3R site will open for submissions on January 18, and the deadline is February 1.
D3R Grand Challenge 2: Error corrections and preliminary results
- 10:42am December 14, 2016
- 1352 views
- gc2
1. Sharp-eyed participants have identified errors, such as nonplanar aromatic rings, in the crystallographic poses we provided for several ligands. We apologize for these errors and are re-refining the structures structures. We hope to get corrected structures to you next week.
2. The graphs below provide a preliminary overview of results for the Stage 1 pose predictions. We expect the RMSDs to change somewhat with the re-refined structures.
GC 2 Ligand 33; Webinar plan
- 01:30pm December 1, 2016
- 1112 views
- gc2
1. You may have noticed that the SMILES string for ligand FXR_033 does not match the ligand in the corresponding crystal structure. …
2. We would like to schedule a web-based conference to discuss this challenge on March 27, 2017. …
Stage 1 closing
- 03:16pm November 29, 2016
- 1155 views
- gc2
The submission window for Stage 1 closed at 5:00 pm Pacific Time today. 38 participants uploaded 143 prediction sets spanning all categories: pose predictions, structure-based scoring, ligand-based scoring, and free energy methods! The data package for Stage 2, which is also the answers to the pose prediction component of Stage 1, is now available.
GC2 24 hour extension
- 03:13pm November 29, 2016
- 1038 views
- gc2
The submission window for your Stage 1 predictions has been extended by 24 hours, to 5pm Pacific Time, Tuesday, November 22.
GC2 Stage 1 open
- 03:11pm November 29, 2016
- 1047 views
- gc2
We just wanted to send a reminder that the D3R website is ready to accept your predictions for Stage 1! Please feel free to contact us with any questions.
Postdoc Opening Announcement 2016
- 03:09pm November 29, 2016
- 1061 views
- d3r
This is to announce a postdoctoral opening in the D3R project. We hope to hire this new team member by early 2017. For information, please see https://t.co/2smqzt7p1M. We would greatly appreciate your sharing this information with colleagues and potential candidates!
Grand Challenge 2 Nov 9 Update
1. We anticipate opening the D3R website for Stage 1 submissions on Monday, November 14, a week before the Nov 21 deadline. 2. Several Example files in the download have been corrected in the current download of submission instructions etc. 3. We also added a README file to the set of Templates to clarify file naming of the free energy submission files. 4. As previously noted, you will be invited to submit a paper about your Grand Challenge 2 results to a special issue of the Journal of Computer-Aided Molecular Design.
Grand Challenge 2 Stage 1 Update
1. Instructions for submitting Stage 1 prediction submissions are now available: http://tinyurl.com/hd8xxh4. 2. Stage 1 predictions are due by 5pm Pacific Time, Monday November 21. We recommend starting the submission process the prior week. 3. This challenge is being renamed Grand Challenge 2. 4. After Grand Challenge 2 is complete, you will be invited to submit a paper about your results for another special issue of the Journal of Computer Aided Molecular Design. Many thanks to Editor-in-Chief Terry Stouch!
Grand Challenge/Planning Survey
- 02:21pm November 29, 2016
- 1124 views
- d3r
Help us design the next challenge! We have contracted to have new Kd values measured for various compounds against a family of protein targets. We would appreciate your input on what types of challenge(s) would be most interesting and useful. Please let us know at https://www.surveymonkey.com/r/BRN23WM
GC2016 Announcement
- 02:18pm November 29, 2016
- 1020 views
- gc2
You are invited to participate in D3R Grand Challenge 2016, which will open September 19!
D3R evaluation results and answer corrections for PL-2016-1
- 02:16pm November 29, 2016
- 1106 views
- pl-2016-1
The two tar files linked here and here provide a corrected set of answers for the PL-2016-1 challenge, and our evaluation of the submitted predictions.
D3R Grand Challenge 2015 overview Paper with Attachment
- 02:13pm November 29, 2016
- 1128 views
- gc2015
Our Grand Challenge 2015 Overview paper is currently under review at JCAMD. In parallel with the review process, we would welcome your comments and particularly corrections to the description of your own methodology and results.
D3R Grand Challenge 2015 Evaluation Results Available
- 01:34pm November 29, 2016
- 1230 views
- gc2015
Files with summary statistics across essentially all submissions are now available at the D3R web-site. To obtain them, please go to the Grand Challenge 2015 page (https://drugdesigndata.org/about/grand-challenge-2015), log in, and choose “Evaluation Results/Download evaluation data” near the top right.
PL-2016-1 Answers Available
- 01:33pm November 29, 2016
- 1043 views
- pl-2016-1
The experimental answers to the challenge are now available at the lower right of this page: https://drugdesigndata.org/about/challenge-pl-2016-1
About
Welcome to the Drug Design Data Resource Community. D3R is funded in part by NIH grant 1U01GM111528 from the National Institute of General Medical Sciences
