ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins.
ProfNet, a method to derive profile-profile alignment scoring functions that improves the alignments of distantly related proteins.
复制标题
ProfNet，一种导出轮廓-轮廓比对评分函数的方法，可改善远缘相关蛋白质的比对。
DOI：
10.1186/1471-2105-6-253
复制
发表时间：
2005-10-14
影响因子：
3
通讯作者：
Elofsson, A
中科院分区：
文献类型：
--
作者：
Ohlson, T;Elofsson, A
轮廓轮廓的方法已经使用了几年，现在检测和比对同源蛋白质。最好的方法是在构建图谱或评分时使用来自氨基酸和取代表的背景分布的信息。这使得这些方法依赖于替代表的质量和选择以及配置文件的构造。在这里，我们介绍了一种新的方法，称为ProfNet，是用来获得一个配置文件的评分函数。该方法优化了相关残基和不相关残基的分数之间的区分，并且使用起来快速且简单。这种新方法推导出的评分函数主要取决于来自训练集的残基的实际比对，并且它不使用关于背景分布的任何附加信息。结果表明，ProfNet提高了相关和不相关残基的歧视。此外，它还可以用于改善远亲蛋白质的比对。在ProfNet的训练中使用超家族相关蛋白质以及与结构对齐残基之间的距离相关的分类器获得最佳性能。新的评分函数和传统的轮廓-轮廓评分函数之间的主要区别是保守残基的平均得分更高的新功能。
Profile-profile methods have been used for some years now to detect and align homologous proteins. The best such methods use information from the background distribution of amino acids and substitution tables either when constructing the profiles or in the scoring. This makes the methods dependent on the quality and choice of substitution table as well as the construction of the profiles. Here, we introduce a novel method called ProfNet that is used to derive a profile-profile scoring function. The method optimizes the discrimination between scores of related and unrelated residues and it is fast and straightforward to use. This new method derives a scoring function that is mainly dependent on the actual alignment of residues from a training set, and it does not use any additional information about the background distribution. It is shown that ProfNet improves the discrimination of related and unrelated residues. Further it can be used to improve the alignment of distantly related proteins. The best performance is obtained using superfamily related proteins in the training of ProfNet, and a classifier that is related to the distance between the structurally aligned residues. The main difference between the new scoring function and a traditional profile-profile scoring function is that conserved residues on average score higher with the new function.
登录
查看更多内容
DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
2.9
作者：
Ohlson, T;Wallner, B;Elofsson, A
通讯作者：
Elofsson, A
影响因子：
5.8
作者：
Pei, JM;Sadreyev, R;Grishin, NV
通讯作者：
Grishin, NV
影响因子：
5.6
作者：
ROST, B;SANDER, C
通讯作者：
SANDER, C