Problems

Technical Problems

Technical problems can be fixed algorithmically. Scientific problems may also be technical, but what differentiates them is that I cannot describe algorithmically how to solve them. Instead, we should take an experimental approach, probably trying at least two different ways, and seeing which works best. Philosophical problems in this context means that I am not even sure how to phrase a scientific question or a testable hypothesis, but I recognize that there is a problem.

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• Out of date catalogs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• SEA index out of date
• activity annotations out of date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
• documentation
• tutorials
• protocols
• describe the pipeline on-line
• get the new paper out

DOCK Blaster

• documentation
• tutorials
• protocols
• get the paper out

DOCK 6.2

• new release
• clean up documentation

DOCK 3.5.54

• prepare new distribution
• documentation
• "collisions"
• inline out of box detection
• ligand internal energy
• write out multiple structures for PLOP

DUD

• more systems
• get the new paper out
• new ways of choosing decoys
• new release

DOCK Tools

• documentation

Infrastructure

• more disk space on line

Scientific Problems

Docking

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