Difference between revisions of "DOCK Release Objectives"
From Rizzo_Lab
| (7 intermediate revisions by 3 users not shown) | |||
| Line 1: | Line 1: | ||
| − | DOCK 6.10 To do list | + | ''DOCK 6.10 To do list'' |
*(1)Update the FMS and FPS test cases | *(1)Update the FMS and FPS test cases | ||
| Line 17: | Line 17: | ||
# <s>Test Brian's rotatable bond fix</s> | # <s>Test Brian's rotatable bond fix</s> | ||
# <s>HMS = NA vs 9999 and implications on dn generic</s> | # <s>HMS = NA vs 9999 and implications on dn generic</s> | ||
| − | # database filter to charge molecule with gasteiger charge | + | # 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 | # score molecule = no, internal energy = yes problem | ||
| + | # Ensure that primary vs. secondary has been removed | ||
POTENTIAL DOCK DESCRIPTORS | POTENTIAL DOCK DESCRIPTORS | ||
| − | # QED | + | # <s>QED</s> |
| − | # logp | + | # <s>logp</s> |
| − | # logS | + | # <s>logS</s> |
| − | # aromatic rings | + | # <s>aromatic rings</s> |
| − | # lipinski alerts/violations | + | # <s>lipinski alerts/violations</s> |
| − | # ligand SASA | + | # <s>ligand SASA</s> |
# ligand desolvation penalty | # ligand desolvation penalty | ||
| − | # polar surface area | + | # <s>polar surface area</s> |
# Rizzo coefficient | # 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. | ||
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.
