Molecular mechanics methods for predicting protein-ligand binding.

By Niu Huang, C. Kalyanaraman, K. Bernacki, Matthew P. Jacobson. Physical Chemistry, Chemical Physics - PCCP, 2006

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Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get” (2009, neutral): “Nevertheless, strain energies often appear to be greater than several kT (Huang et al., 2006).”
Blind tests of RNA–protein binding affinity prediction (2019, methodology): “First, unbound RNA free energies were calculated using a 3D structure-based approach that is standard in protein – protein and protein – small molecule relative binding affinity calculations (18, 32).”
Advances and Challenges in Protein-Ligand Docking (2010, background): “Force field (FF) scoring functions [28,83,84] are based on decomposition of the ligand binding energy into individual interaction terms such as van der Waals (VDW) energies, electrostatic energies, bond stretching/bending/torsional energies, etc.”
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking (2010, neutral): “Indeed, accurately predicting the binding affinities of large sets of diverse protein–ligand complexes remains one of the most important and difficult unsolved problems in computational biomolecular science.”