Ligand Binding Site Comparison — LiBiSCo — a web‐based tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites

Abstract

Interaction between protein and ligands are ubiquitous in a biological cell, and understanding these interactions at the atom level in protein–ligand complexes is crucial for structural bioinformatics and drug discovery. Here, we present a web-based protein–ligand interaction application named Ligand Binding Site Comparison (LiBiSCo) for comparing the amino acid residues interacting with atoms of a ligand molecule between different protein–ligand complexes available in the Protein Data Bank (PDB) database. The comparison is performed at the ligand atom level irrespectively of having binding site similarity or not between the protein structures of interest. The input used in LiBiSCo is one or several PDB IDs of protein–ligand complex(es) and the tool returns a list of identified interactions at ligand atom level including both bonded and non-bonded interactions. A sequence profile for the interaction for each ligand atoms is provided as a WebLogo. The LiBiSco is useful in understanding ligand binding specificity and structural promiscuity among families that are structurally unrelated. The LiBiSCo tool can be accessed through https://albiorix.bioenv.gu.se/LiBiSCo/HomePage.py.