Mining for Bioactive Molecules in Open Databases
Guillem Macip, Júlia Mestres‐Truyol, Pol Garcia‐Segura, Bryan Saldivar‐Espinoza, Santiago Garcı́a-Vallvé, Gerard Pujadas · Methods and principles in medicinal chemistry · 2023
In this chapter we describe the main methods used during a virtual screening (i.e. ADMET and PAINS filtering, protein–ligand docking, pharmacophore search, and shape/electrostatic similarity), determine which open databases are useful during this process (e.g. the Protein Data Bank, the AlphaFold Protein Structure Database, COCONUT, ZINC20, the BindingDB database, PubChem, and DUD-E), and explain how to validate the accuracy of the bioactivity predictions that are obtained.