- 01:32pm May 2, 2017
- 272 views
As you may know, the SAMPL series of blinded prediction challenges focuses on relatively simple, but still difficult, challenges, such as the prediction of hydration free energies, distribution coefficients, host-guest binding affinities, and affinities of small molecules for model binding sites in proteins. SAMPL thus complements D3R, which focus on systems of direct pharmaceutical interest.
Organizers of SAMPL are now developing plans for future challenges and seeking funding to support them. Your input is invited via a brief survey, which is accompanied by a draft roadmap of activities over the next ~5 years.
- 12:28pm March 29, 2017
- 358 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
- 267 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
- 278 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
- 172 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
- 152 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
- 244 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
- 246 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!