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D3R at ACS San Francisco
- 12:28pm March 29, 2017
- 1470 views
- acs
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!
D3R Webinar - March 27, 2017
- 11:00am March 22, 2017
- 1262 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.
PL-2016-1 articles and videos
- 02:20pm March 14, 2017
- 1429 views
- pl-2016-1
Important announcements -- with apologies for cross-postings to GC2 participants!
D3R Webinar, March 27Send Us a Video Seminar about your PL-2016-1 Results!
Special Issue of JCAMD
Release of Protocols and Predictions
GC2 Protocols and PL2016-1
- 02:19pm March 14, 2017
- 1223 views
- gc2, pl-2016-1
More updates, and an invitation!
Sharing of GC2 ProtocolsSharing of GC2 Predictions and Evaluation Scripts
Send Us a Video Seminar about your GC2 Results!
GC2 Protocols, Papers, Etc
- 02:18pm March 14, 2017
- 1352 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.
D3R Grand Challenge 2: Prediction Evaluations Available
- 12:43pm February 23, 2017
- 1232 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.
D3R Grand Challenge 2: Stage 2 Closing and Answers
- 02:20pm February 16, 2017
- 1245 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!
D3R Grand Challenge 2: Dealing with 5-character PDB IDs
- 03:17pm January 31, 2017
- 1212 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.
D3R Grand Challenge 2: Extension of Stage 2 and Stage 1 Pose Evaluations
- 02:35pm January 25, 2017
- 1201 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.
D3R Grand Challenge 2: Crystallographic mtz files now available
- 03:12pm January 20, 2017
- 1181 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.)
D3R Grand Challenge 2: Free Energy Predictions
- 05:01pm January 18, 2017
- 1261 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
- 1109 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
- 1349 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
- 1109 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
- 1151 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
- 1035 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
- 1044 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
- 1057 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!
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
