[Zinc-fans] requesting peer suggestions on docking and duplication

[elite 158]

*Dear Dr. Brian K. Shoichet and Dr. John J. Irwin, *

I wouId like to thank you  for your efforts in making ZINC a noncommercial
database accessible to the docking enthusiasts and students worldwide.


*Dear docking enthusiasts and Zinc fans*,

Here, I present two scenarios, maybe some one might have come across...

*Scenario 1*:

In a certain docking protocol, my concern is primarily of the protonation
states of the ligands in the library (subsets with different pH ranges)
downloaded from ZINC, as I have recently read an article on "The influence
of protonation in protein-ligand docking"

http://www.journal.chemistrycentral.com/content/2/S1/P12

Considering an enzyme that is reported to be optimum at a pH of 7.6-8.0,
which we intend to find inhibitors for, which subset of ZINC compounds do I
chose for docking against my target of interest?

(*Why was there a need to create these subsets based on pH of ligands in
ZINC database? Please educate if time permits*)

*Scenario 2*:
Another question is with handling duplicates in ZINC Libraries. The
automated docking protocol we are currently using requires all the Zinc
comounds (if we are interested to dock a whole subsets of drug-like,
fragment-like etc,) to be present in one single sdf file.

As John wrote a reply sometime back in July 2006 for a query on duplicate
structures, one would definitely not be interested in removing the
duplicates

"... it is perfectly normal to have more than one representation of a
molecule if you combine all the files. For example, imidazole would have one
representation (e.g. protonated) in the p0 "reference" subset, and have the
neutral form in the p1 subset..."

The question is, if we merge all the files into one single giga SDF file,
are the ZINC IDs unique to all the entries, meaning, can we safely traceback
the ligand of interest to its representative pH subset?


With best regards,
Elite158
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