理解相互作用的重要性使得蛋白质相互作用和蛋白质复合物的研究成为突出的。传统上,蛋白质相互作用已经通过实验方法阐明,或者,影响较小,通过蛋白质对接算法的模拟。本文介绍了BiGGER对接算法的特点和应用,站在这两种方法的接口。BiGGER是一种用户友好的对接算法,专门设计用于在仿真的不同阶段合并实验数据,引导搜索正确的结构或帮助评估结果,以便将硬数据的可靠性与模拟的便利性相结合。在这里,BIGGER的应用被分为三个案例研究的说明性应用描述:(案例研究A)没有具体的接触数据可用;(案例研究B)当不同的实验数据(例如,定点诱变,复杂的属性,NMR化学位移扰动映射,电子隧穿)在其中一个伙伴上可用;和(案例研究C)当两个相互作用表面的实验数据可用时,在对接的搜索和/或评估阶段使用。该算法已被广泛使用,证明其在广泛的不同生物学研究领域的有用性。
The importance of understanding interactomes makes preeminent the study of protein interactions and protein complexes. Traditionally, protein interactions have been elucidated by experimental methods or, with lower impact, by simulation with protein docking algorithms. This article describes features and applications of the BiGGER docking algorithm, which stands at the interface of these two approaches. BiGGER is a user-friendly docking algorithm that was specifically designed to incorporate experimental data at different stages of the simulation, to either guide the search for correct structures or help evaluate the results, in order to combine the reliability of hard data with the convenience of simulations. Herein, the applications of BiGGER are described by illustrative applications divided in three
Case Studies: (
Case Study A) in which no specific contact data is available; (
Case Study B) when different experimental data (e.g., site-directed mutagenesis, properties of the complex, NMR chemical shift perturbation mapping, electron tunneling) on one of the partners is available; and (
Case Study C) when experimental data are available for both interacting surfaces, which are used during the search and/or evaluation stage of the docking. This algorithm has been extensively used, evidencing its usefulness in a wide range of different biological research fields.