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首页> 外文期刊>Journal of Molecular Biology >Combination of threading potentials and sequence profiles improves fold recognition.
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Combination of threading potentials and sequence profiles improves fold recognition.

机译：穿线电位和序列图的组合可提高折叠识别度。

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摘要

Using a benchmark set of structurally similar proteins, we conduct a series of threading experiments intended to identify a scoring function with an optimal combination of contact-potential and sequence-profile terms. The benchmark set is selected to include many medium-difficulty fold recognition targets, where sequence similarity is undetectable by BLAST but structural similarity is extensive. The contact potential is based on the log-odds of non-local contacts involving different amino acid pairs, in native as opposed to randomly compacted structures. The sequence profile term is that used in PSI-BLAST. We find that combination of these terms significantly improves the success rate of fold recognition over use of either term alone, with respect to both recognition sensitivity and the accuracy of threading models. Improvement is greatest for targets between 10 % and 20 % sequence identity and 60 % to 80 % superimposable residues, where the number of models crossing critical accuracy and significance thresholds more than doubles. We suggest that these improvements account for the successful performance of the combined scoring function at CASP3. We discuss possible explanations as to why sequence-profile and contact-potential terms appear complementary.
机译：我们使用一组结构相似的蛋白质作为基准，我们进行了一系列穿线实验，旨在通过接触势和序列特征项的最佳组合来识别评分功能。选择基准集以包括许多中等难度的折叠识别靶标，其中BLAST无法检测到序列相似性，但结构相似性广泛。接触电势是基于涉及不同氨基酸对的非局部接触的对数奇数，天然接触与随机压缩结构相反。序列图谱术语是在PSI-BLAST中使用的术语。我们发现，相对于识别灵敏度和穿线模型的准确性，这些术语的组合大大提高了折叠识别的成功率，超过了单独使用两个术语的成功率。对于序列同一性在10％到20％之间以及可重叠残基在60％到80％之间的目标而言，最大的改进是，跨越关键精度和显着性阈值的模型数量增加了一倍以上。我们建议这些改进说明了CASP3组合评分功能的成功执行。我们讨论了有关序列图谱和接触电位术语为何看起来互补的可能解释。

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