Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems

publication · 10 years ago
by Stefano Forli, Maurizio Botta (Università degli Studi di Siena)
Here, we present a setting-up procedure of AutoDock parameters that allows the management of cycle and macrocycle flexibility during the docking process. In particular, the glue dummy atom type is introduced into calculations, and a novel empirical pseudo-Lennard-Jones potential function is applied to describe the intramolecular interactions occurring between two glue dummy atoms. The reliability of such an original protocol is tested by evaluation of 21 cyclic ligands in the corresponding binding site. As a result, the binding mode of 17 ligands is well-reproduced with respect to the X-ray crystallographic structure, with an root-mean-square deviation lower than 2 A for 15 of them.
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