寫在前面
Autodock Vina作為經典的分子對接工具，上手也比較容易，最近學習了一下，特此記錄。
Requirement
- Pymol
2.Plugin ‘GetBox-PyMOL-Plugin’
3.ADFR
4.Autodock Vina
Installation
#源碼下載和安裝
#Vina
https://vina.scripps.edu/downloads/
export PATH=$PATH:/path/to/your/bin # 添加環(huán)境變量
source ~/.bashrc #使生效
#ADFR
https://ccsb.scripps.edu/adfr/downloads/
Prerequisites
1. Pymol in windows
1.1 fetch 7S1S
1.2 刪除水分子 'remove resn HOH' / 'A-remove waters'【如果是預測的結構，不需要去除水分子】
1.3 如果結構是多條鏈的話，刪除不關注的鏈，此時刪除B鏈，'remove chain B'
1.4 pymol中檢查結合位點是否有氨基酸突變或缺失
1.5 使用getbox來獲取口袋參數(shù)?！驹斠妑ef2】
#獲得的口袋參數(shù)如下
--center_x -31.9 --center_y -43.7 --center_z -7.1 --size_x 2
5.8 --size_y 29.8 --size_z 20.6
1.6 刪除完所有的小分子配體，并保存結構
remove resn MTA+85k
save 7S1S_pro.pdb
2. ADFR in Linux
給受體結構加氫質子化，reduce包包含在ADFR程序中。
reduce 7S1S_pro.pdb > 7S1S_H.pdb
Prepare_receptor 將受體結構的PDB格式轉換成PDBQT格式。
prepare_receptor -r 7S1S_H.pdb -o 7S1S_H.pdbqt
對接參數(shù)文件準備，將參數(shù)寫入txt中，并命名為7S1S_vina.txt
center_x = -31.9
center_y = -43.7
center_z =-7.1
size_x = 25.8
size_y = 29.8
size_z = 20.6
使用Vina進行對接計算。
vina --receptor 7S1S_H.pdbqt --ligand 7s1s_C_MTA.pdbqt --cpu 16 --config 7S1S_vina.txt --out 7S1S_23A_vinaout &
會有九個文件生成，打分最低的即為排名最高的構象。
3. Results
先在linux中轉換格式。
babel -ipdbqt 7s1s_C_MTA_out.pdbqt -osdf 7s1s_vina_out.sdf
將對接后的'sdf'文件和原始的結構文件'7s1s.pdb'一起載入pymol中，其中排名第一的構象和試驗解出來的構象十分一致，證明Vina的結果有很高的可靠性。
Tips： How to obtain a correct Mol2 file?
Please, note that the Mol2 files submitted to SwissDock should contain all the hydrogen atoms of the molecule.
First of all, try the Mol2 file you already have. Most of the Mol2 files will work, whatever their origin. If one fails, you can try one of the following:
- get it from the ZINC Database if the molecule is already known,
- or, if the molecule comes from a PDB file (e.g. a ligand), you can use the UCSF chimera visualization software to open the PDB file, remove all molecules except the one of interest, add hydrogen atoms (using the Tools/Structure Editing/AddH menu), and save it as a Mol2 file,
- or use openbabel to convert a correct 3D file from another format into the Mol2 format,
- or draw the molecule in 2D in Chemaxon Marvin Sketch (free), add hydrogens, generate 3D coordinates and save the molecule in the "Tripos Mol2 (mol2)" format.
This list is not exhaustive. If you have trouble getting a working Mol2 file, please contact us.
Citations
1.https://blog.csdn.net/MurphyStar/article/details/132708694
2.https://github.com/MengwuXiao/GetBox-PyMOL-Plugin/tree/master
3.https://ccsb.scripps.edu/adfr/downloads/
4.https://www.swissdock.ch/howtomol2.php
