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

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Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, via Alcide de Gasperi 2, 53100 Siena, Italy
Cite this: J. Chem. Inf. Model. 2007, 47, 4, 1481–1492
Publication Date (Web):June 22, 2007
https://doi.org/10.1021/ci700036j
Copyright © 2007 American Chemical Society
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    Abstract

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    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 Å for 15 of them.

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     Corresponding author tel.:  +39-0577-234307; fax:  +39-0577-234333; e-mail:  [email protected].

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