Abstract：
Proteins are the fundamental organic macromolecules in living systems that play a key role in a variety of biological functions including immunological detection, intracellular trafficking, and signal transduction. The docking of proteins has greatly advanced during recent decades and has become a crucial complement to experimental methods. Protein-protein docking is a helpful method for simulating protein complexes whose structures have not yet been solved experimentally. This chapter focuses on major search tactics along with various docking programs used in protein-protein docking algorithms, which include: direct search, exhaustive global search, local shape feature matching, randomized search, and broad category of post-docking approaches. As backbone flexibility predictions and interactions in high-resolution protein-protein docking remain important issues in the overall optimization context, we have put forward several methods and solutions used to handle backbone flexibility. In addition, various docking methods that are utilized for flexible backbone docking, including ATTRACT, FlexDock, FLIPDock, HADDOCK, RosettaDock, FiberDock, etc., along with their scoring functions, algorithms, advantages, and limitations are discussed. Moreover, what progress in search technology is expected, including not only the creation of new search algorithms but also the enhancement of existing ones, has been debated. As conformational flexibility is one of the most crucial factors affecting docking success, more work should be put into evaluating the conformational flexibility upon binding for a particular case in addition to developing new algorithms to replace the rigid body docking and scoring approach.
摘要：
蛋白质是生命系统中的基本有机大分子，在包括免疫检测在内的各种生物学功能中起着关键作用。细胞内贩运，和信号转导。近几十年来，蛋白质的对接技术取得了很大进展，并已成为实验方法的重要补充。蛋白质-蛋白质对接是模拟尚未通过实验解决其结构的蛋白质复合物的有用方法。本章重点介绍主要的搜索策略以及蛋白质-蛋白质对接算法中使用的各种对接程序，其中包括：直接搜索，详尽的全局搜索，局部形状特征匹配,随机搜索，和广泛类别的对接后方法。由于高分辨率蛋白质-蛋白质对接中的骨架灵活性预测和相互作用仍然是整体优化背景下的重要问题，我们提出了几种处理骨干灵活性的方法和解决方案。此外,用于柔性骨干对接的各种对接方法，包括ATTRACT,FlexDock,FLIPDock,Haddock,RosettaDock,FiberDock,等。,连同他们的评分功能，算法，优势,并讨论了局限性。此外，预计搜索技术会有什么进步，不仅包括创建新的搜索算法，还包括增强现有的搜索算法，已经被辩论了。由于构象灵活性是影响对接成功的最关键因素之一，除了开发新的算法来代替刚体对接和评分方法外，还应该进行更多的工作来评估特定情况下结合时的构象灵活性。
