Dear all,
I would like to know if MOE has the capabilities to carry out flexible docking. What I mean by this is when you allow the binding site (only the residues at the binding site) to be flexible during the docking. I know other software can do this however I was wondering if MOE could also do it? If anyone has experience with this i would greatly appreciate it.
Thanks.
Hmm I only use MOE for viewing, but people say iti isn't neccesairly have the best docking system. Have you tried PLANTS? The rotatable chains are easily set up in the conf file
Yes, MOE is capable of flexible docking, i.e. with flexible sidechains.
In the -menu, you may choose a method for refining the initially docked pose, for example based on a forcefield; select under "Refinement" the option "Forcefield", then click on "Configure" directly next to it. In the following menu (named "Configure Forcefield Refinement" or similar, depending on your MOE-version), you can choose between:
a) an entirely fixed, i.e. unflexible protein, by activating the option "Receptor: Fix"
b) a partially flexible protein, by deactivating "Receptor: Fix"; the additional option "Tether" allows you to choose the degree of moving space for the receptor's sidechains.
All remaining details can be found in the (quite helpful) MOE-manual.
Cheers! Thomas
Hi Tomas,
Thanks for the answer! I will have a further look at the manual and will repost if i have any more trouble if that's ok!
Thanks again,
Danielle
I am using MOE since last three year, but honestly speaking it supports the rigid docking, where the receptor becomes rigid and various possible conformations of molecule or ligand get docked on the selected residues.
