Section: New Results

Updates for the atomic typization software

Participants : Maria Kadukova, Sergei Grudinin.

We have additionally validated Knodle – our atomic typization software – on an extensive set of more than 300,000 small molecules based on the LigandExpo database. Knodle workflow involves machine-learning based "models" for different atoms, this year we retrained several of them on the updated version of PDBBindCN database. These results were published in Journal of Chemical Information and Modeling [45]. We also added functions that add missing hydrogen atoms to the molecules. Knodle was used to classify ligand atoms into different types in our protein-ligand interactions scoring function.