Difference between revisions of "DOCK Release Objectives"
From Rizzo_Lab
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# <s>HMS = NA vs 9999 and implications on dn generic</s> | # <s>HMS = NA vs 9999 and implications on dn generic</s> | ||
# HMS pruning in database filter | # HMS pruning in database filter | ||
| − | # database filter to charge molecule with gasteiger charge | + | # database filter to charge molecule with gasteiger charge (or do we want recharge as a query for all runs??) |
# score molecule = no, internal energy = yes problem | # score molecule = no, internal energy = yes problem | ||
# Ensure that primary vs. secondary has been removed | # Ensure that primary vs. secondary has been removed | ||
Latest revision as of 11:52, 15 July 2024
DOCK 6.10 To do list
- (1)Update the FMS and FPS test cases
- (2)Change variables in the FMS and FPS
- (3)Merge all the changes with the latest CVS version for testing
- (4)Update the DOCK 6.9 HTM file
- (5)Perform the descriptor tests
- (6)Check in the changes to DOCK CVS Tree
Developer To Do:
-
Test Courtney's orienting fixx -
Test Brian's rotatable bond fix -
HMS = NA vs 9999 and implications on dn generic - HMS pruning in database filter
- database filter to charge molecule with gasteiger charge (or do we want recharge as a query for all runs??)
- score molecule = no, internal energy = yes problem
- Ensure that primary vs. secondary has been removed
POTENTIAL DOCK DESCRIPTORS
-
QED -
logp -
logS -
aromatic rings -
lipinski alerts/violations -
ligand SASA - ligand desolvation penalty
-
polar surface area - Rizzo coefficient
POST- DOCK 6.10 release to-dolist
RDKIT
- label in the header of the mol2 that the molecule has a covalent warhead
- We want to eventually add energy score to the pruned dumped mol2 file during D3N
- Add more sophisticated code that outputs the reason why molecules are rejected in the header of the mol2.
