Template selection for placement is extremely important as some experimental fragment poses clash with templates from other fragment hits. I'm thinking there could be a hierarchy of templates to test with the goal of increasing base compound placement success and therefore elaborations of those bases.
Potential pipeline for a given base compound, template, parenthit1, and parenthit2:
Assert that there is no clash with the template for both parent hits.
If there is a clash, change template to the apo structure of the parent hit with the previous clash. Check for clash with both parent hits.
If there is a clash then, throw an Warning. Then proceed with energy minimisation of template around fragment with a less worse clash (determined by distance of closest ligand atom to protein residue).
Template selection for placement is extremely important as some experimental fragment poses clash with templates from other fragment hits. I'm thinking there could be a hierarchy of templates to test with the goal of increasing base compound placement success and therefore elaborations of those bases.
Potential pipeline for a given base compound, template, parenthit1, and parenthit2: