I am using MOE for homology modelling of an enzyme but the model contain too many outliers. So I applied different force-fields which minimized outliers. My question is on whether applying different force-fields on a homology model will effect the structure and function of that enzyme and also whether it will further effect the docking of ligands/drugs?
After energy minimization with default settings, still there were too many outliers. so I followed energy minimization using different force-fields due to which I was successful in reducing outliers but my question is that whether it will affect the quality of homology model for docking or not?
Dear Sohaid,
First of all, you must run a long enough MD simulation to check weather your Homology Model is stable in terms of structure and energy..and then and only then you go for docking or any further steps you want to perform.
Secondly, YES, of course different force field provide significant alterations in results. In different force-fields ...parameters such as bond length and partial charges are different which in theory force a molecule to behave differently. so primarily, before performing MD simulation of a homology model you must research and read about force-fields to chose wisely the one which fits you molecule type and depending upon the MD-engine you are about to use. MD-engines like GROMACS provides a wide variety of force-field parameters available to a researcher such as Amber, OPLS, Gromos and CHARMM and many community added ones too. so review carefully and then choose depending upon molecule type and the literature based information.
Good Luck
cheers : Raghav
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Enzymology
- Enzymes