基于colab 分子仿真学习系列-allosteric binding 分子接合运算

• Colab ipynb数据链路: Blind docking with qvina-wContribute to c00jsw00/Blind-Docking-qvina-w-DENV-NS2BNS3 development by creating an account on GitHub.https://colab.research.google.com/drive/1JJgTd9aEp8kKke2-U1KG_NY_-roDj1NS
• 数据相对应文献: Virus Res . 2023 May;329:199092. doi: 10.1016/j.virusres.2023
• 使用方式: conf(dock控制档案)、recn.pdb(zika ns2bns3 protease)、compound01.mol (异位调控抑制剂)上传至colab
• Pdb viwer in colab: 显示反应中心与异位调控作用胺基酸

• import py3Dmol
  
  def drawit2(m,confId=-1):
      mb = Chem.MolToMolBlock(m,confId=confId)
      p = py3Dmol.view(width=400, height=400)
      p.addModel(mb,'sdf')
      p.setStyle({'stick':{}})
      p.setBackgroundColor('0xeeeeee')
      p.zoomTo()
      return p
  
  def DrawComplex(protein,ligand):
      complex_pl = Chem.MolToPDBBlock(Chem.CombineMols(protein,ligand))
      #complex_mol=Chem.CombineMols(receptor,mols[-1])
      view = py3Dmol.view(width=600,height=600)
      view.addModel(complex_pl,'pdb')
      #view.addModel(Chem.MolToMolBlock(mols[0]),'sdf')
      chA = {'chain':['A','B']}
      chB = {'resn':'UNL'}
      view.setStyle(chA,{'cartoon': {'color':'green'}})
      #view.setStyle(chA,{'lines': {}})
      view.addStyle({'chain':'B','resi':[51,75,135]},{'stick':{'colorscheme':'skyblueCarbon'}}) ##reaction center
      #view.addStyle({'chain':'A','resi':[136,138,139,148,150,153,154,157,183,211,214,200]},{'cartoon': {'color':'yellow'}}) ##allosteric site
      view.addSurface(py3Dmol.VDW,{'opacity':0.8}, chB)
      view.setStyle(chB,{'stick':{}})
      view.zoomTo()
      return view  

• 成功完成异位调控抑制剂分子接合预测: