论文标题
使用Haddock2.4 WebServer的信息驱动抗体 - 抗原建模的协议
A protocol for information-driven antibody-antigen modelling with the HADDOCK2.4 webserver
论文作者
论文摘要
近年来，由于其固有的专有人物和技术进步，用于研究和表征它们的方法，因此对抗体的治疗使用巨大。用于治疗目的的抗体的有效设计和工程在很大程度上取决于对调节抗体 - 抗原相互作用的结构原理的了解。可以应用几种实验技术，例如X射线晶体学，冷冻电子显微镜，NMR或诱变分析，但是这些技术通常很昂贵且耗时。因此，诸如分子对接之类的计算方法可以为抗体 - 抗原复合物的表征提供有价值的替代方法。 在这里，我们描述了使用Integrative Modeling Platform Haddock预测抗体 - 抗原复合物的3D结构的方案。该协议包括：1）鉴定属于多变量环的抗体残基，这些抗体残基已知对于结合至关重要，可用于指导对接； 2）根据有关表位残留物的信息的可用性，使用黑线座2.4 Web服务器执行对接的详细步骤。
In the recent years, therapeutic use of antibodies has seen a huge growth, due to their inherent proprieties and technological advances in the methods used to study and characterize them. Effective design and engineering of antibodies for therapeutic purposes are heavily dependent on knowledge of the structural principles that regulate antibody-antigen interactions. Several experimental techniques such as X-ray crystallography, cryo-electron microscopy, NMR or mutagenesis analysis can be applied, but these are usually expensive and time consuming. Therefore computational approaches like molecular docking may offer a valuable alternative for the characterisation of antibody-antigen complexes. Here we describe a protocol for the prediction of the 3D structure of antibody-antigen complexes using the integrative modelling platform HADDOCK. The protocol consists of: 1) The identification of the antibody residues belonging to the hyper variable loops which are known to be crucial for the binding and can be used to guide the docking; 2) The detailed steps to perform docking with the HADDOCK 2.4 webserver following different strategies depending on the availability of information about epitope residues.
