二联体重复模式的纳入提高了跨膜β桶蛋白的拓扑预测。
Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.
机构信息
Memorial Sloan Kettering Cancer Center, New York City, NY, USA.
Stockholm Bioinformatics Center, SciLifeLab, Swedish E-Science Research Center, Stockholm University, Stockholm, SE, 10691, Sweden and.
出版信息
Bioinformatics. 2016 May 15;32(10):1571-3. doi: 10.1093/bioinformatics/btw025. Epub 2016 Jan 21.
UNLABELLED
: Accurate topology prediction of transmembrane β-barrels is still an open question. Here, we present BOCTOPUS2, an improved topology prediction method for transmembrane β-barrels that can also identify the barrel domain, predict the topology and identify the orientation of residues in transmembrane β-strands. The major novelty of BOCTOPUS2 is the use of the dyad-repeat pattern of lipid and pore facing residues observed in transmembrane β-barrels. In a cross-validation test on a benchmark set of 42 proteins, BOCTOPUS2 predicts the correct topology in 69% of the proteins, an improvement of more than 10% over the best earlier method (BOCTOPUS) and in addition, it produces significantly fewer erroneous predictions on non-transmembrane β-barrel proteins.
AVAILABILITY AND IMPLEMENTATION
BOCTOPUS2 webserver along with full dataset and source code is available at http://boctopus.bioinfo.se/
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
未加标签
准确预测跨膜β桶结构仍然是一个悬而未决的问题。在这里，我们提出了 BOCTOPUS2，这是一种改进的跨膜β桶结构的拓扑预测方法，它还可以识别桶域、预测拓扑结构和识别跨膜β-折叠中残基的取向。BOCTOPUS2 的主要新颖之处在于使用了在跨膜β桶中观察到的脂双层和孔面向残基的二联体重复模式。在对 42 个蛋白质基准集的交叉验证测试中，BOCTOPUS2 在 69%的蛋白质中预测出正确的拓扑结构，比最好的早期方法（BOCTOPUS）提高了 10%以上，此外，它对非跨膜β桶蛋白质产生的错误预测要少得多。
可用性和实现
BOCTOPUS2 网络服务器以及完整的数据集和源代码可在 http://boctopus.bioinfo.se/ 获得。
联系人
补充信息
补充数据可在Bioinformatics 在线获得。
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