使用AutoDock4进行对接。

Docking with AutoDock4.

作者信息

Bitencourt-Ferreira Gabriela, Pintro Val Oliveira, de Azevedo Walter Filgueira

机构信息

Escola de Ciências da Saúde, Pontifícia Universidade Católica do Rio Grande do Sul-PUCRS, Porto Alegre, RS, Brazil.

出版信息

Methods Mol Biol. 2019;2053:125-148. doi: 10.1007/978-1-4939-9752-7_9.

DOI:10.1007/978-1-4939-9752-7_9

PMID:31452103

Abstract

AutoDock is one of the most popular receptor-ligand docking simulation programs. It was first released in the early 1990s and is in continuous development and adapted to specific protein targets. AutoDock has been applied to a wide range of biological systems. It has been used not only for protein-ligand docking simulation but also for the prediction of binding affinity with good correlation with experimental binding affinity for several protein systems. The latest version makes use of a semi-empirical force field to evaluate protein-ligand binding affinity and for selecting the lowest energy pose in docking simulation. AutoDock4.2.6 has an arsenal of four search algorithms to carry out docking simulation including simulated annealing, genetic algorithm, and Lamarckian algorithm. In this chapter, we describe a tutorial about how to perform docking with AutoDock4. We focus our simulations on the protein target cyclin-dependent kinase 2.

摘要

AutoDock是最受欢迎的受体-配体对接模拟程序之一。它于20世纪90年代初首次发布，一直在持续开发并适用于特定的蛋白质靶点。AutoDock已应用于广泛的生物系统。它不仅用于蛋白质-配体对接模拟，还用于预测结合亲和力，与几种蛋白质系统的实验结合亲和力具有良好的相关性。最新版本利用半经验力场来评估蛋白质-配体结合亲和力，并在对接模拟中选择能量最低的构象。AutoDock4.2.6有四种搜索算法来进行对接模拟，包括模拟退火、遗传算法和拉马克算法。在本章中，我们描述了一个关于如何使用AutoDock4进行对接的教程。我们将模拟重点放在蛋白质靶点细胞周期蛋白依赖性激酶2上。