DUMM4

Attendees & Time

Date: October 29, 2008, 3:00pm -

Next DUM on DDD

Michael Mysinger talked about improvements to DOCK:

account for solvation during minimization and during single mode
scoreopt_so now outputs solvation energies instead of just percentage desolvations
important bugfix affecting rigid molecules
use /raid1/soft/dock69 or later to get these changes

Michael Mysinger then continued to monopolized the discussion by introducing:

Tools to help running and analyzing dock jobs from the command line: MUD - Michael's Utilities for Docking
Tools to automatically generate docking flexibases and DUD style decoys: Automated Database Preparation

Pascal: /raid6 is now mounted on the QB3 cluster and can be found in /bks/raid6 there.

John: Various changes in ZINC, documented on my blog http://docking.org/. Highlights:

Use of Epik to compute more sensible protonation states and tautomers. First thing being fixed is those ridiculous di-amine cations. Thanks to Christian, Sarah, Michael, Pascal for enabling this.
Lead-like and fragment-like re-definition; new subsets in progress
over 1M compounds depleted (removed) from ZINC due to no longer being available.
correspondingly, millions of new compounds have been added to ZINC.
talk about the "catalog explosion problem" raised by Denise.
ZINC9 will appear in January. I am taking requests.
"dock68" version. We will release "dock69" to coincide with this meeting.

1. The section heading "Errata" is erroneous, and should be "Erratum".