- 12:28pm March 29, 2017
- 738 views
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!
- 11:00am March 22, 2017
- 660 views
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.
- 02:20pm March 14, 2017
- 691 views
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
- 02:19pm March 14, 2017
- 603 views
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!
- 02:18pm March 14, 2017
- 697 views
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.
- 12:43pm February 23, 2017
- 576 views
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.
- 02:20pm February 16, 2017
- 605 views
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!
- 03:17pm January 31, 2017
- 584 views
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.
- 02:35pm January 25, 2017
- 563 views
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
- 03:12pm January 20, 2017
- 574 views
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.)
- 05:01pm January 18, 2017
- 627 views
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
- 01:29pm January 17, 2017
- 500 views
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.
- 10:42am December 14, 2016
- 729 views
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.
- 01:30pm December 1, 2016
- 539 views
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. …
- 03:16pm November 29, 2016
- 579 views
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.
- 03:13pm November 29, 2016
- 442 views
The submission window for your Stage 1 predictions has been extended by 24 hours, to 5pm Pacific Time, Tuesday, November 22.
- 03:11pm November 29, 2016
- 429 views
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.
- 03:09pm November 29, 2016
- 420 views
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!
- 03:06pm November 29, 2016
- 407 views
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.
- 02:24pm November 29, 2016
- 420 views
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!