Problems

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• Out of date catalogs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• SEA index out of date
• activity annotations out of date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

Scientific Problems

Docking

• • treatment of entropy
  • treatment of desolvation
  • treatment of induced-fit effects
  • ligand internal energy