Free ligand-protein interaction

Simulation Studies of Protein-Ligand Interactions 141 Table 2. Table Ligand-protein interaction energies and free energies (kcal/mol). 

In principle, in both slow and fast exchange limits, the analysis of the ligand-protein interaction could be performed by a direct integration of the two well-separated resonances of free and bound ligand and by the analysis of their chemical shift. However, these methods are limited by the broadness of the protein-ligand NMR spectra, and numerical values of association constants are barely obtainable. 

Empirical Free Energy Calculations of Ligand-Protein Crystallographic Complexes. I. Knowledge-Based Ligand-Protein Interaction Potentials Applied to the Prediction of Human Immunodeficiency Virus 1 Protease Binding Affinity. 

Ligand-Protein Interactions Using OWFEG Free Energy Grids. 

Verkhivker, G., Appelt, K., Freer, S.T., Villafranca, J.E. Empirical free eenrgy calculations of ligand-protein crystallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng. 1995, 8, 677-91. 

The full calculation of the ligand-protein interaction free energy in solution, as diagrammed in Fig. 10b, corresponds to the determination of the free energy of solvation of the three separate species and the evaluation of the appropriate difference i.e.,... 

The most accurate and precise scores are invariably obtained from the fully free-energy calculation for ligand-protein interaction. 

Pearlman, D. A. and Charifson, P. S. (2001) Improved scoring of ligand-protein interaction using OWFEG free energy grids. J. Med. Chem. 44, 502-511. 

In the context of ligand-protein interactions we start with the free energy change associated with the following process... 

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