DUMM4

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Attendees & Time

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

Next DUM on DDD

Hardware updates

Software updates

Michael Mysinger talked about improvements to DOCK:

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

Michael Mysinger then continued to monopolized the discussion by introducing:

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

Requests/Improvements

Database updates

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.

Varia

Errata

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

Action Items

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