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TPRpred：一种从蛋白质序列预测TPR、PPR和SEL1样重复序列的工具。

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

作者信息

Karpenahalli Manjunatha R, Lupas Andrei N, Söding Johannes

机构信息

Department of Protein Evolution, Max-Planck-lnstitute for Developmental Biology, Spemannstrasse 35, D-72076 Tübingen, Germany.

出版信息

BMC Bioinformatics. 2007 Jan 3;8:2. doi: 10.1186/1471-2105-8-2.

DOI:10.1186/1471-2105-8-2
PMID:17199898
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC1774580/
Abstract

BACKGROUND

Solenoid repeat proteins of the Tetratrico Peptide Repeat (TPR) family are involved as scaffolds in a broad range of protein-protein interactions. Several resources are available for the prediction of TPRs, however, they often fail to detect divergent repeat units.

RESULTS

We have developed TPRpred, a profile-based method which uses a P-value-dependent score offset to include divergent repeat units and which exploits the tendency of repeats to occur in tandem. TPRpred detects not only TPR-like repeats, but also the related Pentatrico Peptide Repeats (PPRs) and SEL1-like repeats. The corresponding profiles were generated through iterative searches, by varying the threshold parameters for inclusion of repeat units into the profiles, and the best profiles were selected based on their performance on proteins of known structure. We benchmarked the performance of TPRpred in detecting TPR-containing proteins and in delineating the individual repeats therein, against currently available resources.

CONCLUSION

TPRpred performs significantly better in detecting divergent repeats in TPR-containing proteins, and finds more individual repeats than the existing methods. The web server is available at http://tprpred.tuebingen.mpg.de, and the C++ and Perl sources of TPRpred along with the profiles can be downloaded from ftp://ftp.tuebingen.mpg.de/ebio/protevo/TPRpred/.

摘要

背景

四三肽重复（TPR）家族的螺线管重复蛋白作为支架参与广泛的蛋白质-蛋白质相互作用。有几种资源可用于预测TPR，但它们常常无法检测到不同的重复单元。

结果

我们开发了TPRpred，这是一种基于轮廓的方法，它使用依赖P值的分数偏移来纳入不同的重复单元，并利用重复序列串联出现的趋势。TPRpred不仅能检测到类似TPR的重复序列，还能检测到相关的五三肽重复（PPR）和SEL1样重复序列。通过迭代搜索生成相应的轮廓，改变将重复单元纳入轮廓的阈值参数，并根据它们对已知结构蛋白质的性能选择最佳轮廓。我们将TPRpred在检测含TPR蛋白质和描绘其中单个重复序列方面的性能与现有资源进行了基准测试。

结论

TPRpred在检测含TPR蛋白质中的不同重复序列方面表现明显更好，并且比现有方法发现更多的单个重复序列。该网络服务器可在http://tprpred.tuebingen.mpg.de获得，TPRpred的C++和Perl源代码以及轮廓可从ftp://ftp.tuebingen.mpg.de/ebio/protevo/TPRpred/下载。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f9e/1774580/1ff320d7b1dd/1471-2105-8-2-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f9e/1774580/ea5d51b8c555/1471-2105-8-2-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f9e/1774580/998b95f4bfdc/1471-2105-8-2-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f9e/1774580/1ff320d7b1dd/1471-2105-8-2-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f9e/1774580/ea5d51b8c555/1471-2105-8-2-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f9e/1774580/998b95f4bfdc/1471-2105-8-2-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7f9e/1774580/1ff320d7b1dd/1471-2105-8-2-3.jpg

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