【1.1】计算残基暴露程度(freesasa)

github软件下载:http://freesasa.github.io/

一、下载和安装

wget -c http://freesasa.github.io/freesasa-2.0.3.tar.gz
tar -xzf freesasa-2.0.3.tar.gz
cd freesasa-2.0.3

./configure --disable-json --prefix=/data/software/freesasa
make 
make install  

二、使用说明

2.1 输入参数

例子:

[sam@g03 protein]$ freesasa input/6F1H.pdb
## FreeSASA 2.0.3 ##

PARAMETERS
algorithm    : Lee & Richards
probe-radius : 1.400
threads      : 2
slices       : 20

INPUT
source  : input/6F1H.pdb
chains  : ACDB
model   : 1
atoms   : 8988

RESULTS (A^2)
Total   :   57622.06
Apolar  :   31206.08
Polar   :   26415.97
CHAIN A :   14632.95
CHAIN C :   14434.11
CHAIN D :   14612.67
CHAIN B :   13942.34

如果需要更高的精度(use 100 slices per atom instead of the default 20):

freesasa input/6F1H.pdb -n 100

计算SASA用Shrake & Rupley算法, 200 test points, a probe radius of 1.2 Å, 4个线程

freesasa --shrake-rupley -n 200 --probe-radius 1.2 --n-threads 4 3wbm.pdb

使用自定义的配置文件

freesasa --config-file <file> 3wbm.pdb

To use the atomic radii from NACCESS call

freesasa --radii=naccess 3wbm.pdb

Another way to specify a custom set of atomic radii is to store them as occupancies in the input PDB file

freesasa --radius-from-occupancy 3wbm.pdb

2.2 输出例子

  • 除了上次的格式,FreeSASA可以通过 –format 输出每个残基的JSON, XML, PDB, RSA, SASA格式,也可以输出每个残基的SASA。
  • JSON和XML输出结果的内容,可以通过 –output-depth= 选择在atom, residue, chain and structure输出。如果为atom, SASA values are shown for all levels of the structure, including individual atoms. With chain, only structure and chain SASA values are printed (this is the default).
  • The output can include relative SASA values for each residues. To calculate these a reference SASA value is needed, calculated using the same atomic radii. At the moment such values are only available for the ProtOr and NACCESS radii (selected using the option –radii), if other radii are used relative SASA will be excluded (in RSA output all REL columns will have the value ‘N/A’).
  • The reference SASA values for residue X are calculated from Ala-X-Ala peptides in a stretched out configuration. The reference configurations are supplied for reference in the directory rsa. Since these are not always the most exposed possible configuration, and because bond lengths and bond angles vary, the relative SASA values will sometimes be larger than 100 %. At the moment there is no interface to supply user-defined reference values.

(原理暂时不理解,后续再来回顾)

2.2.1 json

freesasa --format=xml --output-depth=residue 3wbm.pdb

输出:

{
  "source":"FreeSASA 2.0",
  "length-unit":"Ångström",
  "results":[
    {
      "input":"3wbm.pdb",
      "classifier":"ProtOr",
      "parameters":{
        "algorithm":"Lee & Richards",
        "probe-radius":1.3999999999999999,
        "resolution":20
      },
      "structures":[
        {
          "chain-labels":"ABCDXY",
          "area":{
            "total":25190.768387067546,
            "polar":13638.391677017404,
            "apolar":11552.376710050148,
            "main-chain":3337.1622502425053,
            "side-chain":21853.606136825045
          },
          "chains":[
            {
              "label":"A",
              "n-residues":86,
              "area":{
                "total":3785.4864049452635,
                "polar":1733.8560208488598,
                "apolar":2051.6303840964056,
                "main-chain":723.34358684348558,
                "side-chain":3062.1428181017791
              }
              "residues":[
                {
                  "name":"THR",
                  "number":"5",
                  "area":{
                    "total":138.48216994006549,
                    "polar":56.887951514571867,
                    "apolar":81.594218425493622,
                    "main-chain":38.898190013033592,
                    "side-chain":99.583979927031905
                  },
                  "relative-area":{
                    "total":104.05152148175331,
                    "polar":113.98106895325961,
                    "apolar":98.093554250413092,
                    "main-chain":96.330336832673567,
                    "side-chain":107.414496739329
                  },
                  "n-atoms":7
               },
            ...
            },
            ...
          ]
        }
      ]
    }
  ]

2.2.2 XML

示例:

freesasa --format=xml 3wbm.pdb

结果:

<?xml version="1.0" encoding="UTF-8"?>
<results xmlns="http://freesasa.github.io/" source="FreeSASA 2.0" lengthUnit="&#xC5;ngstr&#xF6;m">
  <result classifier="ProtOr" input="3wbm.pdb">
    <parameters algorithm="Lee &amp; Richards" probeRadius="1.400000" resolution="20"/>
    <structure chains="ABCDXY">
      <area total="25190.768" polar="13638.392" apolar="11552.377" mainChain="3337.162" sideChain="21853.606"/>
      <chain label="A" nResidues="86">
        <area total="3785.486" polar="1733.856" apolar="2051.630" mainChain="723.344" sideChain="3062.143"/>
      </chain>
      <chain label="B" nResidues="84">
        <area total="4342.334" polar="1957.114" apolar="2385.220" mainChain="853.707" sideChain="3488.627"/>
      </chain>
      <chain label="C" nResidues="86">
        <area total="3961.119" polar="1838.724" apolar="2122.395" mainChain="782.652" sideChain="3178.468"/>
      </chain>
      <chain label="D" nResidues="89">
        <area total="4904.298" polar="2332.306" apolar="2571.991" mainChain="977.459" sideChain="3926.838"/>
      </chain>
      <chain label="X" nResidues="25">
        <area total="4156.455" polar="2919.576" apolar="1236.879" mainChain="0.000" sideChain="4156.455"/>
      </chain>
      <chain label="Y" nResidues="25">
        <area total="4041.076" polar="2856.815" apolar="1184.261" mainChain="0.000" sideChain="4041.076"/>
      </chain>
    </structure>
  </result>
</results>

2.2.3 PDB

后续在补充吧。。

三、我的案例

freesasa input/12E8.pdb -n 100 –depth=residue –format=seq –n-threads=4

SEQ P 206 VAL : 41.73 SEQ P 207 ASP : 97.35 SEQ P 208 LYS : 42.78 SEQ P 209 LYS : 115.82 SEQ P 210 ILE : 2.54 SEQ P 211 VAL : 81.71 SEQ P 212 PRO : 68.03 SEQ P 213 ARG : 157.27 SEQ P 214 ASP : 22.14

第一列代表用的序列模式,第二列是链,第三列是UID,第四列代表残基,最后一列是对应的ASA值

案例2 :

[sam@g03 protein]$ freesasa input/12E8.pdb --format=rsa --n-threads=4  --radii=naccess|head -n 20
REM  FreeSASA 2.0.3
REM  Absolute and relative SASAs for input/12E8.pdb
REM  Atomic radii and reference values for relative SASA: NACCESS
REM  Chains: LHMP
REM  Algorithm: Lee & Richards
REM  Probe-radius: 1.40
REM  Slices: 20
REM RES _ NUM      All-atoms   Total-Side   Main-Chain    Non-polar    All polar
REM                ABS   REL    ABS   REL    ABS   REL    ABS   REL    ABS   REL
RES ASP L   1   131.82  93.8  74.56  75.5  57.26 137.1  27.11  55.0 104.70 114.8
RES ILE L   2    12.14   6.9   9.85   7.4   2.29   5.6   9.85   7.1   2.29   6.3
RES VAL L   3    88.71  58.6  84.43  76.6   4.27  10.4  88.29  76.6   0.42   1.2
RES MET L   4     8.99   4.6   0.00   0.0   8.99  21.5   0.00   0.0   8.99  24.7
RES THR L   5    64.64  46.4  58.92  60.4   5.72  13.7  46.85  61.8  17.79  28.0
RES GLN L   6     7.63   4.3   0.08   0.1   7.56  18.1   0.14   0.3   7.49   5.9
RES SER L   7    82.71  71.0  53.96  73.7  28.75  66.3  47.02  96.9  35.69  52.5
RES GLN L   8    93.00  52.2  91.12  66.7   1.88   4.5  27.93  53.8  65.07  51.5
RES LYS L   9   113.28  56.6 105.29  66.4   7.99  19.1  93.78  80.9  19.50  23.1
RES PHE L  10    86.51  43.4  75.89  47.1  10.62  27.9  76.71  46.5   9.80  28.6
RES MET L  11    47.61  24.6  40.99  27.0   6.62  15.9  47.61  30.3   0.00   0.0

参考资料

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