Centre for Emerging Diseases, Department of Biotechnology, Jaypee Institute of Information Technology, Noida, Uttar Pradesh, India.
Methods Mol Biol. 2024;2780:69-89. doi: 10.1007/978-1-0716-3985-6_5.
Molecular docking is used to anticipate the optimal orientation of a particular molecule to a target to form a stable complex. It makes predictions about the 3D structure of any complex based on the binding characteristics of the ligand and the target receptor usually a protein. It is an exceptionally useful tool, which is used as a model to study how ligands attach to proteins. Docking can also be used for studying the interaction of ligands and proteins to analyze inhibitory efficacy. The ligand may also be a protein, making it possible to study interactions between two different proteins using the numerous docking tools available for basic research on protein interactions. The protein-protein docking is a crucial approach to understanding the protein interactions and predicting the structure of protein complexes that have not yet been experimentally determined. Moreover, the protein-protein interactions can predict the function of target proteins and the drug-like properties of molecules. Therefore, protein docking assists in uncovering insights into protein interactions and also aids in a better understanding of molecular pathways/mechanisms. This chapter comprehends the various tools for protein-protein docking (pairwise and multiple), including their methodologies and analysis of output as results.
分子对接用于预测特定分子与靶标形成稳定复合物的最佳取向。它根据配体和靶受体（通常是蛋白质）的结合特性，对任何复合物的 3D 结构进行预测。这是一种非常有用的工具，可作为研究配体如何附着于蛋白质的模型。对接还可用于研究配体和蛋白质的相互作用，以分析抑制效果。配体也可能是蛋白质，这使得使用众多可用于蛋白质相互作用基础研究的对接工具研究两种不同蛋白质之间的相互作用成为可能。蛋白质-蛋白质对接是理解蛋白质相互作用并预测尚未通过实验确定的蛋白质复合物结构的关键方法。此外，蛋白质-蛋白质相互作用可以预测靶蛋白的功能和分子的类药性。因此，蛋白质对接有助于揭示蛋白质相互作用的见解，并帮助更好地理解分子途径/机制。本章介绍了蛋白质-蛋白质对接（成对和多个）的各种工具，包括它们的方法和输出结果的分析。
