![glide docking tutorial glide docking tutorial](https://img.yumpu.com/40732606/1/500x640/combiglide-quick-start-guide-isp.jpg)
We will rename the ligand as “SO.pdb” just to avoid any kind of confusion. Click on “File” –> “Save Molecule” –> select the molecule –> click “OK”. Open PyMol, and open the downloaded ligand.We will use PyMol for this purpose and never use online converters because they may ruin your ligand file. pdb format, therefore, we have to convert. Since we need the protein and the ligand to be in a.Click on Sodium octanoate and look under “3D Structure” section, click on “Download” and then you will see four different formats for downloading it.
#Glide docking tutorial download#
We can download the structure from the ZINC database also. We are using “sodium octanoate” as a ligand.
#Glide docking tutorial software#
There are also docking software were the score function return positive value, where higher (positive) score represents a better docking pose. In this case, the lower values also represent the best docking. Other score functions like ChemPLP (used in PLANTS and GOLD software) are dimensionless and don't have a direct physical/chemical meaning. In both cases, the score functions are in units of kcal/mol (or energy/mol) and the lower the value is, the better the docking is.
![glide docking tutorial glide docking tutorial](https://www.biorxiv.org/content/biorxiv/early/2020/10/04/2020.10.02.324343/F3.large.jpg)
There are score functions (like those from GLIDE and AUTODOCK) that roughly represent the ligand/protein binding energy.
![glide docking tutorial glide docking tutorial](https://www.macinchem.org/blog/files/fileupload.png)
These score functions are created/modified by the software developers and, in principle, they are not interchangeable: you can not compare two docking studies made with different docking software. Each docking software has its own score function. In a molecular docking, the affinity between a protein and a ligand is determined using what is called score functions.