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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.
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.
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.
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. …
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.
The submission window for your Stage 1 predictions has been extended by 24 hours, to 5pm Pacific Time, Tuesday, November 22.
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.
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!
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.
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!
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
You are invited to participate in D3R Grand Challenge 2016, which will open September 19!
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.
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.
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.
The experimental answers to the challenge are now available at the lower right of this page: https://drugdesigndata.org/about/challenge-pl-2016-1