使用薛定谔计算套件研究蛋白质-肽相互作用。

Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite.

作者信息

Bhachoo Jas, Beuming Thijs

机构信息

Schrödinger, Inc., 120 West 45th Street, 17th Floor, New York, NY, 10036, USA.

出版信息

Methods Mol Biol. 2017;1561:235-254. doi: 10.1007/978-1-4939-6798-8_14.

DOI:10.1007/978-1-4939-6798-8_14

PMID:28236242

Abstract

The Schrödinger software suite contains a broad array of computational chemistry and molecular modeling tools that can be used to study the interaction of peptides with proteins. These include molecular docking using Glide and Piper, relative binding free energy predictions with FEP+, conformational searches using MacroModel and Desmond, and structural refinement using Prime and PrimeX. In this review we provide a comprehensive overview of these tools and describe their potential application in the identification and optimization of peptide ligands for proteins.

摘要

薛定谔软件套件包含一系列广泛的计算化学和分子建模工具，可用于研究肽与蛋白质的相互作用。这些工具包括使用Glide和Piper进行分子对接、使用FEP+预测相对结合自由能、使用MacroModel和Desmond进行构象搜索，以及使用Prime和PrimeX进行结构优化。在本综述中，我们对这些工具进行了全面概述，并描述了它们在识别和优化蛋白质肽配体方面的潜在应用。