Please use this identifier to cite or link to this item: http://hdl.handle.net/20.500.12779/5315
Title: ‘Lennard-Jones potential and dummy atom settings to overcome the AUTODOCK limitation in treating flexible ring systems’
Authors: S., Forli
Botta, Maurizio 
Issue Date: 2007
Project: None 
Journal: JOURNAL OF CHEMICAL INFORMATION AND MODELING
Abstract: 
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 Angstrom for 15 of them.
Description: 
22345
URI: http://hdl.handle.net/20.500.12779/5315
ISSN: 1549-9596
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