Free energy binding

Ajay and Murcko, 1995] Ajay, ajid Murcko, M. Computational methods to predict binding free energy in ligand-receptor complexes. J. Med. Chem. 38 (1995) 4953-4967... 

S. Miyamoto and P. A. Kollman. Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. Proteins, 16 226-245, 1993. 

The confinement term is unique because it alone causes a dependence of the binding free energy on the choice of unit concentration in the standard state the volume available per ligand molecule in the free state, and hence the compression factor, depend on the unit concentration. 

Molecular transformation calculations can be used for computing differ-enr.es in binding free, energy for two ligands by a well-established scheme... 

Hansson, T., Aqvist, J. Estimation of binding free energies for HIV proteinase inhibitors by molecular dynamics simulations. Prot. Eng. 8 (1995) 1137-1144... 

Mark, A. E., Xu, Y., Liu, H., van Gunsteren, W. F. Rapid non-empirical approaches for estimating relative binding free energies. Acta Biochim. Polonica 42 (1995) 525-536... 

Bash P A, U C Singh, F K Brown, R Langridge and P A Kollman 1987. Calculation of the Relat Change in Binding Free-Energy of a Protein-Inhibitor Complex. Science 235 574-576. 

Eriksson M A L, J Pitera and P A Kollman 1999. Prediction of the Binding Free Energies of New TIBO-like HIV-1 Reverse Transcriptase Inhibitors Using a Combination of PROFEC, PB/SA, CMC/MD, and Free Energy Calculations. Journal of Medicinal Chemistry 42 868-881. 

Hansson T and J Aqvist 1995. Estimation of Binding Free Energies for HIV Proteinase Inhibitors b Molecular Dynamics Simulations. Protein Engineering 8 1137-1144. 

In case of the rigid lock-and-key type receptor forming five hydrogen bonds plus two extended electrostatic attractions (Fig. 3a), one mismatched hydrogen bond will result in only a small reduction in overall binding free energy 4.18-8.36 kJ mol (1-2 kcal mol ) out of... 

Figure 1 Thermodynamic cycles for solvation and binding, (a) Solutes S and S in the gas phase (g) and solution (w) and bound to the receptor R in solution, (b) Binding of S to the receptors R and R. The oblique arrows on the left remove S to the gas phase, then transfer it to its binding site on R. This pathway allows the calculation of absolute binding free energies.

To relate the standard binding free energy to free energies that can be obtained from simulations, we use... 

Many applications are concerned only with binding free energy differences. Comparing the binding of two ligands, L and L, to the receptors R and R, we have... 

S Hirono, PA Kollman. Calculation of the relative binding free energy of 2 -GMP and 2 -AMP to ribonuclease T1 using molecular dynamics/free energy perturbation approaches. J Mol Biol 212 197-209, 1990. 

DM Perguson, RJ Radmer, PA Kollman. Determination of the relative binding free energies of peptide inhibitors to the HIV-1 protease. J Med Chem 34 2654-2659, 1991. 

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