hello there,
I want to carry out a screening process via molecular docking, I attempt to carry out self docking of the co-crystallized ligand via MOE, that usually yield RMSD values higher than 2A, can this be due to an internsic problem in the protein itself, or something wrong with my procedure.
Hi,
most probably the docking algorithm in MOE is not optimal to reproduce the co-crystallized pose. You have to change some of the parameters accordingly (e.g. HB, hydrophobic, pi-pi) to fine-tune it.
Try using higher pose-sampling using the placement parameters with higher values. Also retain more poses in rescoring 1 and perform energy minimization with force field. This might help. Alternatively, check if your ligand (and receptor) has proper partial charge assignation, sometimes this is an issue which causes strong differences in docking.
- Badges
- Science topic