Biological Networks and Chemogenomics

The studies on biological networks enable better undestanding of the mechanism of interaction between molecules. Our studies revolve around protein-protein interaction networks which are created using the ligands that they bind to. As a case study, we focus on β-lactamase and Penicillin Binding Protein (PBP) failies. We aim to analyse the relationships between the members of the β-lactamase family through the ligand structures using that they bind to. Our ultimate goal is to characterize novel β-lactamases and discover some indicators that lead to drug resistance.

Chemogenomics combines the chemical properties of ligands with the sequence properties of proteins in order to represent protein-ligand interactions in a better way. Most of the recent protein-ligand interaction prediction methods are based on chemogenomics. What we do is, we investigate the effect of ligand similarity factor and different methods to calculate similarity of small molecules on the task of protein-ligand interaction prediction.