Problems
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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- Out of date catalogs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- SEA index out of date
- activity annotations out of date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