Sometimes, it needs to calculate the binding free energy (e.g. training Vinardo score) according to the Ki, Kd, pKd or pKi values from PDBBind database. Before calculating binding free energy, the International System of Units (SI) is introduced. Most laboratory and literature use mol/dm3, which is the same as mol/L (also named “M”). For example:
mol/m3 = 10−3 mol/dm3 = 10−3 mol/L = 10−3 M = 1 mmol/L = 1 mM.
The "millimolar" and "micromolar" refer to mM and μM (10−3 mol/L and 10−6 mol/L), respectively. About the detail relative information of molar concentration units, please see the website: https://en.wikipedia.org/wiki/Molar_concentration
In this tutorial, the MolAICal (https://doi.org/10.1093/bib/bbaa161) provides an easy way to calculate binding free energy if the value of Ki, Kd, pKd or pKi is given.
2. Materials
2.1. Software requirement
1) MolAICal: https://molaical.github.io
2.2. Example files
1) All the necessary tutorial files are downloaded from:
https://github.com/MolAICal/tutorials/tree/master/010-pkdEnergy
For more detailed procedures, please go to https://molaical.github.io, and click the section named "Tutorials" in the left part of webpage. Once "Tutorials" open, you can freely find pdf file about this tutorial (see Figure 1):
You can repeat this tutorial according to the content of pdf file.
