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== Software updates == | == Software updates == | ||
Michael Mysinger | 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 to | 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]] | |||
===Requests/Improvements=== | ===Requests/Improvements=== | ||
| Line 37: | Line 40: | ||
== Errata == | == Errata == | ||
1. The section heading "Errata" is erroneous, and should be "Erratum". | 1. The section heading "Errata" is erroneous, and should be "Erratum". | ||
== Action Items == | == Action Items == | ||
Latest revision as of 20:11, 8 October 2012
Attendees & Time
Date: October 29, 2008, 3:00pm -
Next DUM on DDD
Hardware updates
Software updates
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
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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