CONCEPT Lab, Istituto Italiano di Tecnologia (IIT), Via E. Melen, 83, I-16152 Genova, Italy.
J Chem Theory Comput. 2021 Nov 9;17(11):7271-7280. doi: 10.1021/acs.jctc.1c00789. Epub 2021 Oct 15.
Protein-protein docking typically consists of the generation of putative binding conformations, which are subsequently ranked by fast heuristic scoring functions. The simplicity of these functions allows for computational efficiency but has severe repercussions on their discrimination capabilities. In this work, we show the effectiveness of suitable descriptors calculated along short scaled molecular dynamics runs in recognizing the nearest-native bound conformation among a set of putative structures generated by the HADDOCK tool for eight protein-protein systems.
蛋白质-蛋白质对接通常包括生成假定的结合构象,然后通过快速启发式评分函数对其进行排序。这些函数的简单性允许计算效率,但对其判别能力有严重影响。在这项工作中,我们展示了在识别由 HADDOCK 工具生成的一组假定结构中最接近天然结合构象时,沿短尺度分子动力学运行计算的合适描述符的有效性,针对八个蛋白质-蛋白质系统。