Computational Biology Program, The University of Kansas, Lawrence, Kansas, United States of America.
PLoS One. 2022 May 17;17(5):e0267531. doi: 10.1371/journal.pone.0267531. eCollection 2022.
Membrane proteins are significantly underrepresented in Protein Data Bank despite their essential role in cellular mechanisms and the major progress in experimental protein structure determination. Thus, computational approaches are especially valuable in the case of membrane proteins and their assemblies. The main focus in developing structure prediction techniques has been on soluble proteins, in part due to much greater availability of the structural data. Currently, structure prediction of protein complexes (protein docking) is a well-developed field of study. However, the generic protein docking approaches are not optimal for the membrane proteins because of the differences in physicochemical environment and the spatial constraints imposed by the membranes. Thus, docking of the membrane proteins requires specialized computational methods. Development and benchmarking of the membrane protein docking approaches has to be based on high-quality sets of membrane protein complexes. In this study we present a new dataset of 456 non-redundant alpha helical binary interfaces. The set is significantly larger and more representative than the previously developed sets. In the future, it will become the basis for the development of docking and scoring benchmarks, similar to the ones for soluble proteins in the Dockground resource http://dockground.compbio.ku.edu.
尽管膜蛋白在细胞机制中起着重要作用，并且在实验蛋白质结构测定方面取得了重大进展，但它们在蛋白质数据库（PDB）中的代表性仍然严重不足。因此，在膜蛋白及其复合物的情况下，计算方法特别有价值。开发结构预测技术的主要重点一直是可溶性蛋白，部分原因是结构数据的可用性大大增加。目前，蛋白质复合物（蛋白质对接）的结构预测是一个成熟的研究领域。然而，由于物理化学环境的差异和膜带来的空间限制，通用的蛋白质对接方法并不适用于膜蛋白。因此，膜蛋白的对接需要专门的计算方法。基于高质量的膜蛋白复合物数据集，开发和基准测试膜蛋白对接方法是必要的。在这项研究中，我们提出了一个新的数据集，包含 456 个非冗余的α螺旋二元界面。与之前开发的数据集相比，该数据集要大得多，也更具代表性。将来，它将成为开发对接和评分基准的基础，类似于 http://dockground.compbio.ku.edu 中可溶性蛋白质的基准。
