Journal
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
Volume 25, Issue 20, Pages 13819-13824Publisher
ROYAL SOC CHEMISTRY
DOI: 10.1039/d3cp01388j
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This study introduces a new drug design approach that combines metadynamics free energy methods and experimental structural information to identify ligand poses on protein surfaces.
Structure-based drug design protocols may encounter difficulties to investigate poses when the biomolecular targets do not exhibit typical binding pockets. In this study, by providing two concrete examples from our labs, we suggest that the combination of metadynamics free energy methods (validated against affinity measurements), along with experimental structural information (by X-ray crystallography and NMR), can help to identify the poses of ligands on protein surfaces. The simulation workflow proposed here was implemented in a widely used code, namely GROMACS, and it could straightforwardly be applied to various drug-design campaigns targeting ligands' binding to protein surfaces.
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