Protein Ligand Binding Affinity

Calculates the protein ligand binding affinity of a given PDB structure with a docked ligand.

The binding affinity of a protein and a ligand is a measure for how well a given protein structure can bind a ligand. This can be important to judge how well a ligand is able to bind into a structure, for example, to find the most potent inhibitor of an enzyme.

The affinity is calculated with Prodigy-Lig, a structure-based method for the prediction of binding affinity in protein-small ligand complexes. The tool uses Gibbs free energy in kcal/mol to measure the binding affinity. The lower (more negative) the value, the stronger the binding.

Input: PDB structure.

Requirements:The file must contain exactly one ligand, which needs to be chain H with the name UNL. This is automatically set using the Add SDF to PDB node (see Structure). Otherwise, it needs to be set by hand. The PDB file can contain more than one chain, but not more than one ligand.

Output: Binding affinity as float.

Citations:

Vangone A, Schaarschmidt J, Koukos P, Geng C, Citro N, Trellet M, Xue L, Bonvin A.: Large-scale prediction of binding affinity in protein-small ligand complexes: the PRODIGY-LIG web server. Bioinformatics

Kurkcuoglu Z, Koukos P, Citro N, Trellet M, Rodrigues J, Moreira I, Roel-Touris J, Melquiond A, Geng C, Schaarschmidt J, Xue L, Vangone A, Bonvin AMJJ.: Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2. J Comput Aided Mol Des 32(1):175-185 (2017).