Free Energies from Docking
Flare 2.0 revision 34140
fkcombu
Rdkit 2018.09.01
calculation method normal
Quality Normal
Max poses 10
Pool Size 1.00
Population Size 1.00
pH 4.5
Ligands were read from file with Flare, minimised protonated to a pH of 4.5 and minimised with Flare. They were then docked to, 2HHN with only retaining one docking pose. The resulting ligand positions were saved and used to find the maximum common substructure between ligand and available crystal structures of GC3. Matched crystal structures were then used to aligned the docked compounds to the crystal compounds using fkcombu. Aligned structures with their respective crystals were then read back into Flare for a second round of docking calculations to pdb structure 5QC4. Top scoring poses were checked to see if binding mode was consistent with known crystal structures. Then the LF dG score was recorded and pose was saved.
yes
no