Pairwise Additivity and Three-Body Contributions for Density Functional Theory-Based Protein-Ligand Interaction Energies.

ABSTRACT: The prediction of protein-ligand binding energies is crucial in computer-assisted drug design. This property can be calculated in a straightforward fashion as the difference in the energies between a binding site-ligand complex and the separated binding site and ligand. Often, though, there is value in knowing how different amino acid residues in the protein binding site interact with the ligand. In this case, the interaction energy can be calculated as the sum of pairwise energies between each amino acid residue in the binding site and the ligand, and the sum of these energies is often equated with the total interaction energy. The validity of this pairwise additivity approximation can be assessed by experimental evidence, such as double-mutant cycles. In this work, we test the pairwise a

SUBMITTER: Schulze CAE 

PROVIDER: S-EPMC10945476 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature