摘要：OEChem不仅是一个强大的数据整合工具，而且还是强大的蛋白-配体相互作用分析工具。本文以最近上市的ABL别构抑制剂Asciminib（ABL001）与ABL的复合物结构PDB 5MO4为例，演示了如何用oechem进行相互作用分析，以及自定义卤键相互作用的可选项，然后再用oedepict进行可视化，本文还演示了如何以文本的方式输出相互作用信息。

abemaciclib

前言

OEChem不仅是一个强大的数据整合工具，而且还是强大的蛋白-配体相互作用分析工具。本文以最近上市的ABL别构抑制剂Asciminib（ABL001）与ABL的复合物结构PDB 5MO4为例，演示了如何用oechem进行相互作用分析，以及自定义卤键相互作用的参数，然后再用oedepict进行相互作用可视化。

操作步骤

下载生成的图片

Asciminib-ABL interaction Asciminib-ABL- nteraction with pi
上节代码的执行结果 将面对边的pi-pi相互作用夹角放宽10度的执行结果

输出文字版的相互作用信息

大多数很多情况下，你只是需要将相互作用可视化，或者判断是否有存在预想的相互作用，而不需要输出所有的相互作用类型。如果您确实需要输出全部的信息，那也是很简单的。

首先先定义几个函数以便将相互作用信息打印出来:

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def GetResidueName(residue):
    return "%3s %4d %s" % (residue.GetName(), residue.GetResidueNumber(), residue.GetChainID())
 
 
def GetInteractionString(inter):
 
    fragstrs = []
    for frag in [inter.GetBgnFragment(), inter.GetEndFragment()]:
        if frag is None:
            continue
        fragtype = frag.GetComponentType()
        if fragtype == oechem.OELigandInteractionHintComponent():
            fragstrs.append("ligand:" + " ".join(sorted(str(a) for a in frag.GetAtoms())))
        if fragtype == oechem.OEProteinInteractionHintComponent():
            fragstrs.append("protein:" + " ".join(sorted(str(a) for a in frag.GetAtoms())))
 
    return " ".join(sorted(f for f in fragstrs))
 
 
def PrintResidueInteractions(asite, residue):
 
    ligatomnames = set()
    for inter in asite.GetInteractions(oechem.OEHasResidueInteractionHint(residue)):
        ligfrag = inter.GetFragment(oechem.OELigandInteractionHintComponent())
        if ligfrag is None:
            continue
        for latom in ligfrag.GetAtoms():
            ligatomnames.add(str(latom))
 
    if len(ligatomnames) != 0:
        print(GetResidueName(residue), ": ", " ".join(sorted(a for a in ligatomnames)))
 
 
def PrintLigandAtomInteractions(asite, atom):
 
    resnames = set()
    for inter in asite.GetInteractions(oechem.OEHasInteractionHint(atom)):
        profrag = inter.GetFragment(oechem.OEProteinInteractionHintComponent())
        if profrag is None:
            continue
        for patom in profrag.GetAtoms():
            residue = oechem.OEAtomGetResidue(patom)
            resnames.add(GetResidueName(residue))
 
    if len(resnames) != 0:
        print(atom, ":", " ".join(sorted(r for r in resnames)))

将分子内、分子间的各种相互作用类型（包括各种contact）全部打印出来:

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print("Number of interactions:", asite.NumInteractions())
for itype in oechem.OEGetActiveSiteInteractionHintTypes():
    numinters = asite.NumInteractions(oechem.OEHasInteractionHintType(itype))
    if numinters == 0:
        continue
    print("%d %s :" % (numinters, itype.GetName()))
 
    inters = [s for s in asite.GetInteractions(oechem.OEHasInteractionHintType(itype))]
    print("\n".join(sorted(GetInteractionString(s) for s in inters)))

结果如下：

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Number of interactions: 128
80 bio:active-site:contact :
ligand: 0Cl protein:5796 C
ligand: 0Cl protein:5797 O
ligand: 0Cl protein:5799 C
ligand: 0Cl protein:5800 C
ligand: 0Cl protein:5856 C
ligand: 0Cl protein:5858 C
ligand: 0Cl protein:5871 N
ligand: 0Cl protein:5875 C
ligand: 0Cl protein:6428 C
ligand: 3 C protein:4264 N
ligand: 6 C protein:6345 C
ligand: 6 C protein:6346 O
ligand: 6 C protein:7101 C
ligand: 7 N protein:7754 O
ligand: 8 C protein:7031 C
ligand: 8 C protein:7400 O
ligand: 8 C protein:7754 O
ligand: 9 C protein:5904 C
ligand: 9 C protein:7031 C
ligand: 9 C protein:7400 O
ligand:10 C protein:5874 O
ligand:10 C protein:5904 C
ligand:10 C protein:6342 O
ligand:10 C protein:7208 O
ligand:11 C protein:6342 O
ligand:12 C protein:5874 O
ligand:12 C protein:6342 O
ligand:13 C protein:4389 C
ligand:13 C protein:7031 C
ligand:13 C protein:7400 O
ligand:14 N protein:7208 O
ligand:15 O protein:4342 C
ligand:15 O protein:4345 C
ligand:15 O protein:4389 C
ligand:15 O protein:7031 C
ligand:15 O protein:7400 O
ligand:16 C protein:7032 C
ligand:16 C protein:7208 O
ligand:17 C protein:4342 C
ligand:17 C protein:4387 C
ligand:17 C protein:4389 C
ligand:18 C protein:4387 C
ligand:18 C protein:6976 C
ligand:19 C protein:6976 C
ligand:20 C protein:5872 C
ligand:20 C protein:5875 C
ligand:20 C protein:6366 S
ligand:20 C protein:6378 C
ligand:20 C protein:6428 C
ligand:21 C protein:5872 C
ligand:21 C protein:5875 C
ligand:21 C protein:6362 C
ligand:21 C protein:6365 C
ligand:21 C protein:6366 S
ligand:21 C protein:6378 C
ligand:21 C protein:7208 O
ligand:22 O protein:6428 C
ligand:22 O protein:6429 C
ligand:22 O protein:6976 C
ligand:24 N protein:5874 O
ligand:24 N protein:6341 C
ligand:24 N protein:6342 O
ligand:25 N protein:5882 C
ligand:25 N protein:7778 O
ligand:26 C protein:5882 C
ligand:26 C protein:5883 C
ligand:26 C protein:5884 O
ligand:27 C protein:4264 N
ligand:27 C protein:5902 C
ligand:28 C protein:6428 C
ligand:29 F protein:4408 C
ligand:29 F protein:4463 C
ligand:29 F protein:6837 C
ligand:30 F protein:4385 C
ligand:30 F protein:4386 O
ligand:30 F protein:4387 C
ligand:30 F protein:4402 N
ligand:30 F protein:4403 C
ligand:30 F protein:4463 C
ligand:30 F protein:5858 C
3 bio:active-site:hbond:protein2ligand :
ligand: 7 N protein:7754 O
ligand:15 O protein:7400 O
ligand:25 N protein:7778 O
2 bio:active-site:hbond:ligand2protein :
ligand:14 N protein:7208 O
ligand:24 N protein:6342 O
25 bio:active-site:hbond:protein-intra-molecular :
protein:4262 N protein:7625 O
protein:4314 O protein:5906 O
protein:4330 O protein:4383 N
protein:4341 N protein:7883 O
protein:4344 O protein:4402 N
protein:4354 O protein:4421 N
protein:4386 O protein:4459 N
protein:4405 O protein:4469 N
protein:4405 O protein:4474 O
protein:5735 O protein:5794 N
protein:5755 O protein:5813 N
protein:5778 O protein:5852 N
protein:5797 O protein:5871 N
protein:5816 O protein:5886 O
protein:5855 O protein:5895 N
protein:5874 O protein:7208 O
protein:5906 O protein:7400 O
protein:6310 N protein:6364 O
protein:6328 O protein:6361 N
protein:6346 O protein:7592 O
protein:6354 N protein:7658 O
protein:6375 O protein:6423 N
protein:6375 O protein:6439 N
protein:7754 O protein:8135 O
protein:8018 O protein:8135 O
13 bio:active-site:hbond:non-ideal-protein-intra-molecular :
protein:4264 N protein:7871 O
protein:4265 N protein:7625 O
protein:4330 O protein:4367 N
protein:4386 O protein:4442 N
protein:5840 O protein:5881 N
protein:5886 O protein:5923 N
protein:6339 N protein:7778 O
protein:6366 S protein:6375 O
protein:6993 O protein:7883 O
protein:7592 O protein:7871 O
protein:7592 O protein:8210 O
protein:7871 O protein:8210 O
protein:7883 O protein:8135 O
1 bio:active-site:hbond:unpaired-ligand-acceptor :
ligand:23 O ligand:23 O
2 bio:active-site:hbond:unpaired-protein-acceptor :
protein:5884 O protein:5884 O
protein:6357 O protein:6357 O
1 bio:active-site:halogen:protein-nucleophile :
ligand: 0Cl protein:5797 O
1 bio:active-site:halogen:ligand-intra-molecular :
ligand: 0Cl ligand:22 O

可以发现，总共发生了128个相互作用，并列出了具体的相互作用类型，比如其中第136行就显示出在蛋白与配体之间有一个卤键相互作用。这个相互作用我们可以从生成的图片里找到。除了分子内相互作用之外，其它的OEChem计算的相互作用已经呈现在Oedepict绘制的图片里面了。

拓展应用

OEChem强大的相互作用分析不仅可以用于视觉分析，还可以用来对docking结果进行后处理，比如过滤出满足特定相互作用模式的化合物。

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