Memdock: an α-helical membrane protein docking algorithm
Memdock: an α-helical membrane protein docking algorithm
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DOI：
10.1093/bioinformatics/btw184
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发表时间：
2016-08-15
期刊：
影响因子：
5.8
通讯作者：
Wolfson, Haim J.
中科院分区：
文献类型：
--
作者：
Hurwitz, Naama;Schneidman-Duhovny, Dina;Wolfson, Haim J.
动机：广泛的基本生物过程是由膜蛋白介导的。尽管它们的数量和重要性很大，但在蛋白质数据库中保存的所有3D蛋白质结构中，只有不到1%是膜蛋白质。这主要是由于结晶这类蛋白质或进行核磁共振光谱分析所面临的挑战。更重要的是，只有少数已知结构的膜蛋白-蛋白质复合体。因此，开发对接膜蛋白的计算工具是至关重要的。对接球状蛋白的方法很多，但专门针对膜蛋白的对接方法很少。结果：我们提出了一种新的对接α-螺旋膜蛋白的算法Memdock，该算法考虑了对接的脂类双层环境，并对对接候选对象进行了提炼和排序。实验结果表明，与标准的蛋白质-蛋白质对接算法相比，该算法在对接精度和候选排序上都有较大的提高。
Motivation: A wide range of fundamental biological processes are mediated by membrane proteins. Despite their large number and importance, less than 1% of all 3D protein structures deposited in the Protein Data Bank are of membrane proteins. This is mainly due to the challenges of crystallizing such proteins or performing NMR spectroscopy analyses. All the more so, there is only a small number of membrane protein-protein complexes with known structure. Therefore, developing computational tools for docking membrane proteins is crucial. Numerous methods for docking globular proteins exist, however few have been developed especially for membrane proteins and designed to address docking within the lipid bilayer environment.Results: We present a novel algorithm, Memdock, for docking alpha-helical membrane proteins which takes into consideration the lipid bilayer environment for docking as well as for refining and ranking the docking candidates. We show that our algorithm improves both the docking accuracy and the candidates ranking compared to a standard protein-protein docking algorithm.