Problems: Difference between revisions
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= Technical Problems = | = Technical Problems = | ||
== ZINC == | == ZINC == | ||
** | * Molecule duplication | ||
** treatment of protonation and tautomerization | * Incorrect representation | ||
** | * Missing representation | ||
* Out of date catalogs | |||
* Broken molecules | |||
* Probably incorrect enumeration/sampling of stereochemistry both R/S and E/Z | |||
* incorrect treatment of protonation and tautomerization in some cases | |||
* search way too slow | |||
* SEA index out of date | |||
* activity annotations out of date | |||
* links to supplier web sites sometimes broken | |||
{{TOCright}} | {{TOCright}} | ||
Revision as of 21:39, 12 February 2009
Technical Problems
ZINC
- Molecule duplication
- Incorrect representation
- Missing representation
- Out of date catalogs
- Broken molecules
- Probably incorrect enumeration/sampling of stereochemistry both R/S and E/Z
- incorrect treatment of protonation and tautomerization in some cases
- search way too slow
- SEA index out of date
- activity annotations out of date
- links to supplier web sites sometimes broken
Cluster
- it is too easy to overload
- Offspring's backplane has issues
- Node O/S update - Michael has ideas
- bjork needs to be rebuilt
- garbage still needs a 4->5 upgrade
- switch in 508 not correctly negotiating with workstations
DOCK 3.5.54
- collisions
- out of box detection
- ligand internal energy
DOCK 6
Scientific Problems
Docking
- treatment of entropy
- treatment of desolvation
- treatment of induced-fit effects
- ligand internal energy