A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions.
A benchmark server using high resolution protein structure data, and benchmark results for membrane helix predictions.
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DOI：
10.1186/1471-2105-14-111
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发表时间：
2013-03-27
影响因子：
3
通讯作者：
Church WB
中科院分区：
文献类型：
--
作者：
Rath EM;Tessier D;Campbell AA;Lee HC;Werner T;Salam NK;Lee LK;Church WB
螺旋膜蛋白对于细胞与其环境的相互作用至关重要。预测蛋白质氨基酸序列中膜螺旋的位置提供了对其结构和功能的实质性理解，并在测序的基因组中鉴定膜蛋白。目前还没有一个全面的基准工具来评估预测方法，也没有出版物比较所有可用的预测工具。目前的基准文献已经过时，因为最近确定的膜蛋白结构不包括在内。目前的文献也仅限于全球评估，因为以前没有进行过用于预测特定类别膜蛋白的专门基准。我们在http://sydney.edu.au/pharmacy/sbio/software/TMH_benchmark.shtml上提供了一个基准服务器，该服务器使用最近的高分辨率蛋白质结构数据来全面评估现有膜螺旋预测方法的准确性。服务器还允许用户比较由新颖方法生成的上传的预测，从而允许将这些新颖方法与由服务器比较的所有现有方法进行比较。基准度量包括膜螺旋位置和方向的预测的灵敏度和特异性，以及许多其他指标。该服务器允许定制评估，例如评估特定螺旋膜蛋白亚型的预测方法性能。我们报告自定义基准测试的结果，说明如何服务器可用于专门的基准测试。哪种预测方法是性能最好的方法取决于哪种测量方法被基准化。OCTOPUS膜螺旋预测方法始终是我们进行的基准测试中所有测量中性能最高的方法之一。基准服务器允许对现有的和新的膜螺旋预测方法进行一般和专业评估。用户可以使用该基准服务器来确定最适合用户需要执行的预测类型的方法，无论是一般的全基因组注释还是特定类型的螺旋膜蛋白的预测。新预测方法的创建者可以使用此基准服务器来评估其新方法的性能。基准服务器将是一个有价值的工具，研究人员寻求从大型和不断增长的蛋白质序列数据库中提取更复杂的信息。
Helical membrane proteins are vital for the interaction of cells with their environment. Predicting the location of membrane helices in protein amino acid sequences provides substantial understanding of their structure and function and identifies membrane proteins in sequenced genomes. Currently there is no comprehensive benchmark tool for evaluating prediction methods, and there is no publication comparing all available prediction tools. Current benchmark literature is outdated, as recently determined membrane protein structures are not included. Current literature is also limited to global assessments, as specialised benchmarks for predicting specific classes of membrane proteins were not previously carried out. We present a benchmark server at http://sydney.edu.au/pharmacy/sbio/software/TMH_benchmark.shtml that uses recent high resolution protein structural data to provide a comprehensive assessment of the accuracy of existing membrane helix prediction methods. The server further allows a user to compare uploaded predictions generated by novel methods, permitting the comparison of these novel methods against all existing methods compared by the server. Benchmark metrics include sensitivity and specificity of predictions for membrane helix location and orientation, and many others. The server allows for customised evaluations such as assessing prediction method performances for specific helical membrane protein subtypes. We report results for custom benchmarks which illustrate how the server may be used for specialised benchmarks. Which prediction method is the best performing method depends on which measure is being benchmarked. The OCTOPUS membrane helix prediction method is consistently one of the highest performing methods across all measures in the benchmarks that we performed. The benchmark server allows general and specialised assessment of existing and novel membrane helix prediction methods. Users can employ this benchmark server to determine the most suitable method for the type of prediction the user needs to perform, be it general whole-genome annotation or the prediction of specific types of helical membrane protein. Creators of novel prediction methods can use this benchmark server to evaluate the performance of their new methods. The benchmark server will be a valuable tool for researchers seeking to extract more sophisticated information from the large and growing protein sequence databases.
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影响因子：
3
作者：
Ganapathiraju M;Balakrishnan N;Reddy R;Klein-Seetharaman J
通讯作者：
Klein-Seetharaman J
影响因子：
2.9
作者：
JONES, DT;TAYLOR, WR;THORTON, JM
通讯作者：
THORTON, JM
影响因子：
64.8
作者：
Oldham, Michael L.;Khare, Dheeraj;Chen, Jue
通讯作者：
Chen, Jue
影响因子：
2.4
作者：
Cuthbertson, JM;Doyle, DA;Sansom, MSP
通讯作者：
Sansom, MSP
影响因子：
64.8
作者：
Efremov, Rouslan G.;Sazanov, Leonid A.
通讯作者：
Sazanov, Leonid A.