Docking algorithms require each atom to have a charge and an atom type that describes its properties. However, the PDB structure lacks these. So, we have to prep the protein and ligand files to include these values along with the atomic coordinates. Furthermore, for flexible ligand docking, we should also define ligand bonds that are rotatable. All this will be done in a tool called AutoDock Tools (adt).
依次点选Grid-Grid box将会在蛋白上画出一个长方体,并且有一个弹出框。在弹出框中,拖拽刻度线查看长方体的变化,完成设置。在这个例子中,我们知道结合位点,就选取以其为中心的一个小空间。设置Spacing (angstrom)为1埃 (这实际是一个换算系数, 相当于步长; 默认为0.375,是C-C单键长度的1/4,最大为1。spacing值与(各个维度上的点的数目+1)的乘机就是长方体Grid box的大小)。在我们调整的过程中,可以看到随着这个数值的变大,立方体也被放大了。另外我们设置x,y,z center为16,25,4,number of points in (x,y,z)-dimension为30,30,30(最大为126,必须为偶数,AutoDock会自动再每一维再加一个点)。记下我们设置的这些点,下面会用到。
在刻度转盘处点击右键会弹出一个窗口,输入数字回车即可设置GRID的中心坐标和大小。较大的number of points in (xyz)-dimension和较小的Spacing会增加搜索的精度,同时需要花费更多的计算时间。
设置受体的柔性残基:在ADT中依次点选Flexible Residues-Input-Choose Macromolecule-1hsg_prot; select-select from string-Residue: ARG8-Add-Dismiss, 8号ARG氨基酸残基就被选中了。
再依次点选Flexible Residues-Choose Torsions in Currently Selected Residues将选择的残基标记为柔性残基并设置可扭转的数量。在分子显示窗口中分别点击两个残基上CA和CB原子之间的建,使之变为非扭转的(紫色显示),这样两个残基中的32个键中有6个是可扭转的。这里设置配体的柔性残基或者使CA-CB的键为刚性都是可选操作。放在教程中只是用来展示怎么操作的,无其它指导意义。
在ADT中定义此化合物为配体,以便ADT为其计算局部电荷(partial charges)和设置可旋转配体键。依次点选Ligand-input-Choose-indinavir-Select Molecule for AutoDock4。这时会有一个弹出框显示ADT所做的操作,包括合并非极性氢(只在添加了的情况下)、计算电荷电量和设置旋转键。然后点选Ligand-Output-Save as PDBQT存储结果。
indinavir.pdbqt为只加了极性氢的结果
indinavir_all_h.pdbqt为加了所以氢的结果
查看ADT检测出的旋转键,依次点选Ligand-Torsion Tree-Choose Torsions,可以看到Number of rotatable bonds=14/32。
The key results in a docking log are the docked structures found at theend of each run, the energies of these docked structures and theirsimilarities to each other. The similarity of docked structures ismeasured by computing the root-mean-square-deviation, rmsd, between the coordinates of the atoms. The docking results consist ofthe PDBQ of the Cartesian coordinates of the atoms in the dockedmolecule, along with the state variables that describe this dockedconformation and position.