Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht 3584CH, the Netherlands.
Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Padualaan 8, Utrecht 3584CH, the Netherlands.
J Mol Biol. 2018 Dec 7;430(24):5246-5256. doi: 10.1016/j.jmb.2018.11.005. Epub 2018 Nov 9.
We report the first membrane protein-protein docking benchmark consisting of 37 targets of diverse functions and folds. The structures were chosen based on a set of parameters such as the availability of unbound structures, the modeling difficulty and their uniqueness. They have been cleaned and consistently numbered to facilitate their use in docking. Using this benchmark, we establish the baseline performance of HADDOCK, without any specific optimization for membrane proteins, for two scenarios: true interface-driven docking and ab initio docking. Despite the fact that HADDOCK has been developed for soluble complexes, it shows promising docking performance for membrane systems, but there is clearly room for further optimization. The resulting set of docking decoys, together with analysis scripts, is made freely available. These can serve as a basis for the optimization of membrane complex-specific scoring functions.
我们报告了第一个由 37 个具有不同功能和折叠的靶标组成的膜蛋白-蛋白对接基准，这些结构是根据一系列参数选择的，如无约束结构的可用性、建模难度和独特性。它们已经过清理和一致编号，以方便对接使用。使用这个基准，我们在没有针对膜蛋白进行任何特定优化的情况下，建立了 HADDOCK 的基线性能，用于两种情况：真实界面驱动的对接和从头开始的对接。尽管 HADDOCK 是为可溶性复合物开发的，但它在膜系统中显示出了有前途的对接性能，但显然还有进一步优化的空间。生成的对接诱饵集以及分析脚本都是免费提供的。这些可以作为优化膜复合物特异性评分函数的基础。
