Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: Here,  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 beten 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 ll-reproduced with respect to the X-ray crystallographic structure, with an root-mean-square deviation lor than 2 A for 15 of them.
['Stefano Forli', 'Maurizio Botta']
I am writing a research paper on a idea Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems.
[{"from": "human", "value": "I am writing a research paper on a idea Lennard-Jones Potential and Dummy Atom Settings to Overcome the AUTODOCK Limitation in Treating Flexible Ring Systems."}, {"from": "gpt", "value": "Thats a unique idea.You should consider the following idea to enhance your idea so that it would impact uniquely: Here,  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 beten 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 ll-reproduced with respect to the X-ray crystallographic structure, with an root-mean-square deviation lor than 2 A for 15 of them."}]