【4.2.3】蛋白质二级结构预测--psipred

PSI-PRED用到了两级神经网络。它首先用PSI-BLAST迭代搜索序列数据库,并根据搜索出来的蛋白质建立目标蛋白质的profile (序列谱),从而将蛋白质氨基酸序列用profile来表示,对每个位点最终选择前后共15个位点组成一个窗口(windows)输入神经网络进行二级结构预测。

官网: http://bioinf.cs.ucl.ac.uk/psipred/

一、安装

1.1 下载安装psipred

cd /data/software/psipred
wget -c http://bioinfadmin.cs.ucl.ac.uk/downloads/psipred/psipred.4.02.tar.gz

tar -xzvf psipred.4.02.tar.gz

cd psipred/src
make
make install

执行文件在/data/software/psipred/psipred/bin中

cd /data/software/psipred/psipred/BLAST+
vim runpsipredplus

set dbname = /data/database/uniprot/uniref/uniref90
set ncbidir = /data/software/ncbi-blast-2.7.1+/bin

[sam@c01 data]$ which psiblast /data/software/ncbi-blast-2.7.1+/bin/psiblast

1.2 测试

cd /data/software/psipred/psipred/example

../BLAST+/runpsipredplus example.fasta

Ru  nning PSI-BLAST with sequence example.fasta ...
Predicting secondary structure...
Pass1 ...
Pass2 ...
Cleaning up ...
Final output file: example.horiz
Finished.

结果文件:

example.horiz 为序列水平展示的结果 example.ss 为一行一个残基, 输出每个残基对应coil, helix, strand

注:

如果序列太短,获得不了比对的结果,建议20个残基以上。

1.3 其他用法

psipass2的参数说明:

psipass2 weights_p2.dat 1 1.0 1.0 output.ss2 input.ss > output.horiz
  • Argument 2: No of filter iterations。This controls the amount of “smoothing” that is carried out on the final prediction. The recommended setting is 1, but it may be worth trying higher values to increase the level of smoothing.

  • Argument 3&4: Helix/Strand Decision constants。These options control the bias for helix (Arg3) and strand (Arg4) predictions. The default values are equal to 1.0, but if you know your protein is, for example, mostly comprised of beta strands then you can increase the bias towards beta strand prediction. For example:

  • psipass2 weights_p2.dat 1 1.0 1.3 output.ss2 input.ss > output.horiz

  • increases the bias towards beta strand prediction by approximately 30%.

注:

从PSIPRED V4.0开始,我们不再认为有必要对与PSI-BLAST一起使用的序列数据库进行过滤以除去低复杂度区域,跨膜区域和卷曲螺旋片段。 因此,搜索数据库可以是任何大型的非冗余蛋白质序列数据库,建议使用UNIREF90( http://www.uniprot.org/help/uniref )。

参考资料

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