DUMM2

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Attendees & Time

  1. John Irwin
  2. Sarah Boyce
  3. Peter Kolb
  4. Rafaela Ferreira
  5. Alessandro Nascimento
  6. Denise Teotico
  7. Gabe Rocklin
  8. Oliv Eidam
  9. Hao Fan
  10. Francesco Colizzi

Date: July 09, 2008, 4:00pm-5:20pm

Next DUM on August 06, 2008 at 4pm

Hardware updates

Software updates

getrandom.pl

John: getrandom.pl program (and website) to select molecules randomly from ZINC. If run directly, this program should be executed on korn or any other machine that has access to ZINC.

rebuildit2.pl

John: rebuildit2.pl to rebuild pre-cavitation ZINC entries. This is being hooked behind DOCK Blaster, upload, and subset web services.

Requests/Improvements

Database updates

John: recently completed ZINC8 release, including a full export of many subsets.

John: loaded lab molecules L99A binders, non-binders, etc. Still in beta - i.e. must be reviewed carefully.

John: a database of natural products is available from the ZINC web site. 90K natural products or derivatives of natural products that are commercially available.

Varia

Flexible receptor docking

Sarah reported on how to use receptor flexibility with DOCK.

HEI database generation

Peter talked about the ways to generate a database of high energy intermediates (HEIs).

Action Items

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