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PROPKA:蛋白结构pKa预测程序

PROPKA是基于蛋白3D结构预测可离子化基团pKa的程序,是非常快的基于经验的蛋白残基pKa计算1程序. 程序由哥本哈根大学的Jan Jensen组开发维护. 现有版本有2.0, 3.0, 3.1 三个版本, 其中2.0版本比较老, 主程序由Fortran实现; 3.0在pdb2pqr中使用,但不能用于小分子配体处理; 3.1版可以处理小分子配体, 主页说在处理纯蛋白结构时3.0和3.1无差别, 但有人说还是有差异的 2. 2.0版本提供在线服务器.

经实际使用比较, propka3.0和propka3.1的确还是有差异的..不仅仅是ref 2 里提及的His的问题. 另外输出格式略有不同, 不能直接给pdb2pqr使用, 伤心ing…

propka3.0

安装和运行

安装十分方便, 直接从git复制过来就好了:

git clone git@github.com:jensengroup/propka-3.0.git

复制后运行:

python propka.py protein.pdb 就可以了, 注意是python3可以. 一般指定pH使用 -p pH就好了

运行选项:

自己读paper 3 研究选项吧…

Options:
  -h, --help            show this help message and exit
  -f FILENAMES, --file=FILENAMES
                        read data from <filename>, i.e. <filename> is added to
                        arguments
  -r REFERENCE, --reference=REFERENCE
                        setting which reference to use for stability
                        calculations [neutral/low-pH]
  -c CHAINS, --chain=CHAINS
                        creating the protein with only a specified chain,
                        note, chains without ID are labeled 'A' [all]
  -t THERMOPHILES, --thermophile=THERMOPHILES
                        defining a thermophile filename; usually used in
                        'alignment-mutations'
  -a ALIGNMENT, --alignment=ALIGNMENT
                        alignment file connecting <filename> and <thermophile>
                        [<thermophile>.pir]
  -m MUTATIONS, --mutation=MUTATIONS
                        specifying mutation labels which is used to modify
                        <filename> according to, e.g. N25R/N181D
  -v VERSION_LABEL, --version=VERSION_LABEL
                        specifying the sub-version of propka [Jan15/Dec19]
  -z, --verbose         sleep during calculations
  -q, --quiet           sleep during calculations
  --mute                sleep during calculations
  -s, --silent          not activated yet
  --verbosity           level of printout - not activated yet
  --protonation=PROTONATION
                        setting protonation scheme
  -p PH, --pH=PH        setting pH-value used in e.g. stability calculations
                        [7.0]
  --window=WINDOW       setting the pH-window to show e.g. stability profiles
                        [0.0, 14.0, 1.0]
  --grid=GRID           setting the pH-grid to calculate e.g. stability
                        related properties [0.0, 14.0, 0.1]
  --mutator=MUTATOR     setting approach for mutating <filename>
                        [alignment/scwrl/jackal]
  --mutator-option=MUTATOR_OPTIONS
                        setting property for mutator [e.g. type="side-chain"]
  -d, --display-coupled-residues
                        Displays alternative pKa values due to coupling of
                        titratable groups
  --print-iterations    Displays the pKa iterations in the Tanford-Roxby
                        scheme

propka3.1

安装和使用

也从github复制到本地即可. 官网说明是使用python setup.py install --user进行安装到~/.local/bin, 建议另行指定安装位置,例如安装到~/bin, 使用--install-scripts ~/bin指定.

git clone git@github.com:jensengroup/propka-3.1.git
python setup.py install --user --install-scripts ~/bin
propka31 1hpx.pdb

但实际我在mac上运行时报错.

running install
error: can't combine user with prefix, exec_prefix/home, or install_(plat)base

不知为何.. 解决办法就是..直接复制scripts/propka31.py出来使用就好了..注意会调用propka文件夹的内容,所以最好将该文件夹弄到python模块搜索路径里(如果要通处使用的话..)

选项

细节可以参考文献 4.

Options:
  -h, --help            show this help message and exit
  -f FILENAMES, --file=FILENAMES
                        read data from <filename>, i.e. <filename> is added to
                        arguments
  -r REFERENCE, --reference=REFERENCE
                        setting which reference to use for stability
                        calculations [neutral/low-pH]
  -c CHAINS, --chain=CHAINS
                        creating the protein with only a specified chain.
                        Specify " " for chains without ID [all]
  -i TITRATE_ONLY, --titrate_only=TITRATE_ONLY
                        Treat only the specified residues as titratable. Value
                        should be a comma-separated list of "chain:resnum"
                        values; for example: -i "A:10,A:11"
  -t THERMOPHILES, --thermophile=THERMOPHILES
                        defining a thermophile filename; usually used in
                        'alignment-mutations'
  -a ALIGNMENT, --alignment=ALIGNMENT
                        alignment file connecting <filename> and <thermophile>
                        [<thermophile>.pir]
  -m MUTATIONS, --mutation=MUTATIONS
                        specifying mutation labels which is used to modify
                        <filename> according to, e.g. N25R/N181D
  -v VERSION_LABEL, --version=VERSION_LABEL
                        specifying the sub-version of propka [Jan15/Dec19]
  -p PARAMETERS, --parameters=PARAMETERS
                        set the parameter file
                        [/Users/Hom/MyGit/propka-3.1/propka/propka.cfg]
  -z, --verbose         sleep during calculations
  -q, --quiet           sleep during calculations
  -s, --silent          not activated yet
  --verbosity           level of printout - not activated yet
  -o PH, --pH=PH        setting pH-value used in e.g. stability calculations
                        [7.0]
  -w WINDOW, --window=WINDOW
                        setting the pH-window to show e.g. stability profiles
                        [0.0, 14.0, 1.0]
  -g GRID, --grid=GRID  setting the pH-grid to calculate e.g. stability
                        related properties [0.0, 14.0, 0.1]
  --mutator=MUTATOR     setting approach for mutating <filename>
                        [alignment/scwrl/jackal]
  --mutator-option=MUTATOR_OPTIONS
                        setting property for mutator [e.g. type="side-chain"]
  -d, --display-coupled-residues
                        Displays alternative pKa values due to coupling of
                        titratable groups
  -l, --reuse-ligand-mol2-files
                        Reuses the ligand mol2 files allowing the user to
                        alter ligand bond orders
  -k, --keep-protons    Keep protons in input file
  --protonate-all       Protonate all atoms (will not influence pKa
                        calculation)

  1. 蛋白pKa计算-维基 ↩

  2. Why do propka3 (only protein) and propka 3.1 (protein and ligand) produce different results? ↩ ↩2

  3. 1. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions: J. Chem. Theory Comput., 2011, 7 (2), pp 525–537
    2. Very Fast Prediction and Rationalization of pKa Values for Protein-Ligand Complexes: PROTEINS: Structure, Function, and Bioinformatics 73:765-783 (2008)
    3. Very Fast Empirical Prediction and Rationalization of Protein pKa Values: PROTEINS: Structure, Function, and Bioinformatics 61:704-721 (2005) ↩

  4. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values: J. Chem. Theory Comput., 2011, 7 (7), pp 2284–2295 ↩


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