Inserm U1134, Paris, France Univ. Paris Diderot, Sorbonne Paris Cité, UMR_S 1134, Paris, France Institut National De La Transfusion Sanguine, Paris, France Laboratory of Excellence GR-Ex, Paris, France.
Bioinformatics. 2016 Aug 15;32(16):2548-50. doi: 10.1093/bioinformatics/btw208. Epub 2016 Apr 19.
: The experimental determination of membrane protein orientation within the lipid bilayer is extremely challenging, such that computational methods are most often the only solution. Moreover, obtaining all-atom 3D structures of membrane proteins is also technically difficult, and many of the available data are either experimental low-resolution structures or theoretical models, whose structural quality needs to be evaluated. Here, to address these two crucial problems, we propose OREMPRO, a web server capable of both (i) positioning α-helical and β-sheet transmembrane domains in the lipid bilayer and (ii) assessing their structural quality. Most importantly, OREMPRO uses the sole alpha carbon coordinates, which makes it the only web server compatible with both high and low structural resolutions. Finally, OREMPRO is also interesting in its ability to process coarse-grained protein models, by using coordinates of backbone beads in place of alpha carbons.
http://www.dsimb.inserm.fr/OREMPRO/ CONTACT: : guillaume.postic@univ-paris-diderot.fr or jean-christophe.gelly@univ-paris-diderot.fr
Supplementary data are available at Bioinformatics online.
：在脂质双层中确定膜蛋白取向的实验测定极具挑战性，因此计算方法通常是唯一的解决方案。此外，获得膜蛋白的全原子 3D 结构在技术上也很困难，并且许多可用数据要么是实验低分辨率结构，要么是理论模型，其结构质量需要进行评估。在这里，为了解决这两个关键问题，我们提出了 OREMPRO，这是一个能够进行（i）在脂质双层中定位α螺旋和β折叠跨膜结构域，以及（ii）评估其结构质量的网络服务器。最重要的是，OREMPRO 使用仅有的α碳原子坐标，这使其成为唯一与高分辨率和低分辨率都兼容的网络服务器。最后，OREMPRO 还能够处理粗粒度的蛋白质模型，方法是使用骨干珠的坐标代替α碳原子。
http://www.dsimb.inserm.fr/OREMPRO/
guillaume.postic@univ-paris-diderot.fr 或 jean-christophe.gelly@univ-paris-diderot.fr
补充数据可在“Bioinformatics”在线获取。
