We want to test some enhanced scoring function in docking of flexible ligands. Our main bootleneck is the automatic analysis of ligand flexibility, i.e., which parts or fragments of the molecule to consider rigid and which not, for example, in terms of flexible dihedral angles. We wonder if there are open source libraries (not another programs) which we could use for such purpose.
PS: I got information that there is a possibility to do this with Chemistry Development Kit (Egon Willighagen)
PS2: Another option seems to be OpenBabel since it can detect rotatable bonds
I said library not another program
sorry for the confusion, I have updated the question
anyway, could autodock do that?
in term of library - try OpenEye Omega
and yes, autodock can do that
OpenEye Omega can only generate conformers, but I do not see information related to fragment/flexibility analysis
Sorry, I don't understand. There is bond - it can be aromatic thou not flexible. All others are mostly flexible even in the rings. OpenEye Tools can clearly state which bond is flexible and which are not.