各位老师好，使用autodock vina对接后输出的亲合能结果排名，如图，想请教下为什么前几个数值都是一样的...
9、隐藏蛋白质所有氢键，选择Protein后面的H-sticks10、仅显示与小分子连接位置，点击Bindingsite后面的S-...
autodock vina 结果分析我们需要在对蛋白和小分子autodock vina 结果分析的PDB文件预处理,生成PDBQT文件同时包含以上信息和PDB文件中的原子坐标信息。进一步地对于“柔性配体docking”,autodock vina 结果分析我们还需要定义配体的柔性部分和刚性部分。所有这些都可以通过软件AutoDock Tools (adt)来完成。 ===准备受体蛋白...
AutoDock Vina (Vina) achieved a very high docking‐success rate, p ^ , but give a rather low correlation coefficient, R , for binding affinity with respect to experiments. This low correlation can be an obstacle for ranking of ligand‐binding affinity, which is the main objective of docking...
vina --config config1.txt 结果分析: 用pymol打开cluster1_hypericin_out.pdbqt看结果 以下为详细设置和操作: 1. 首先用MGLtools准备蛋白和小分子的坐标文件(pdbqt) 蛋白质:加氢(Add all hydrogens or just non-polar hydrogens. Merge non-polar hydrogens and their charges with their parent carbon atom)...
autodock vina 1.对接环境配置 在ubuntu中使用root权限安装在anaconda3 #进入root权限 sudo su #下载安装anaconda3,过程中均选yes。 wgethttps://mirrors.tuna.tsinghua.edu.cn/anaconda/archive/Anaconda3-2020.11-Linux-x86_64.sh sh Anaconda3-2020.11-Linux-x86_64.sh ...
Thebinding pose and affinity between a ligand and enzyme are veryimportant pieces of information for computer-aided drug design. Inthe initial stage of a drug discovery project, this information isoften obtained by using molecular docking methods. Autodock4 and AutodockVina are two commonly used op...
Protein-ligand docking code autodock vina from vina.scripps.edu - autodock-vina/src/main/main.cpp at 07a6294a4a957527def41e67544bdbb504aaf50a · jandom/autodock-vina
2.3 Input: --receptor arg rigid part of the receptor (PDBQT) --flex arg flexible side chains, if any (PDBQT) --ligand arg ligand (PDBQT) --batch arg batch ligand (PDBQT) --scoring arg (=vina) scoring function (ad4, vina or vinardo) Search space (required): --maps arg affinity ...
关键词:虚拟筛选;分子对接;AutodockVina;DiscoveryStudio;抑制剂 中图分类号:Q518.2文献标识码:A文章编号:1672-5565(2012)-04-248-06 Comparisonofautodockvinaanddiscoverystudioinvirtual screeningforantibioticresistanceproteininhibitors HUANGYong 1 ,CHENChen ...