Lennard-Jones potential and dummy atom settings to overcome the AUTODOCK limitation in treating flexible ring systems

被引：41

作者：

Forli, Stefano ^{[1
]}

Botta, Maurizio ^{[1
]}

机构：

[1] Univ Siena, Dipartimento Farmacochim Tecnol, I-53100 Siena, Italy

来源：

JOURNAL OF CHEMICAL INFORMATION AND MODELING | 2007年 / 47卷 / 04期

关键词：

D O I：

10.1021/ci700036j

中图分类号：

R914 [药物化学];

学科分类号：

100701 ;

摘要：

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.

引用

页码：1481 / 1492

页数：12

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