基于AlphaFold2和分子动力学模拟预测抗体可变区结构

Prediction of Antibody Variable Region Structure Based on AlphaFold2 and Molecular Dynamics Stimulation

开发了基于AlphaFold2和分子动力学模拟预测抗体可变区结构的设计流程。使用AlphaFold2分别建模抗体轻链和重链可变区结构,通过序列比对选出方向模板,从而确定轻链与重链之间的位置,最后借助分子动力学模拟对结构进行优化。选取蛋白质结构数据库中最新发布的30个抗体作为测试,建模结果与真实结构之间的平均RMSD可达到0.077 nm,TMscore可达0.93。结果表明该流程可以准确地预测抗体可变区结构。

A design process for predicting the structure of antibody variable region based on AlphaFold2 and molecular dynamics simulation was developed.AlphaFold2 was used to model the variable region structure of the light chain and the heavy chain of the antibody,and the direction template was selected through sequence alignment to determine the position between the light chain and the heavy chain.Finally,the structure was optimized by molecular dynamics simulation.Selecting 30 newly published antibodies in the protein structure database as the test,the average RMSD between the modeling results and the real structure can reach 0.077 nm,and the TMscore can reach 0.93.The results show that the process can accurately predict the structure of antibody variable region.