Binding free energy calculating

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. 

X. Xou, Y. Sun, and I. Kuntz, Inclusion of solvation in ligand binding free energy calculations using the generalized-Bom model, J. Am. Chem. Soc. 121 8033 (1999). 

The examples discussed here show that the new LIE parametrization of Ref. 26, while reliable for a number of systems, could not be the final word in the development of this type of approximate binding free energy calculations. As we will see below there may be more examples of ligand-receptor systems that don t fit the simple picture of Figure 1. 

M. D. Paulsen and R. L. Omstein, Binding free energy calculations for P450cam-... 

Figure 4. The free energy calculation results for all mutations. The numbers in italics are the relative binding free energies calculated from experimental Kj values. Other numbers are the relative binding free energies from the simulations. Units are kcal/mol.

Hou T, Wang J, Li Y, Wang W (2011) Assessing the performance of the MM/PBSA and MM/ GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model 51(l) 69-82... 

Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model. 

Verkhivker GM (2004) Computational analysis of ligand binding dynamics at the intermolecular hot spots with the aid of simulated tempering and binding free energy calculations, Mol J Graph Model, 22(5) 335-348... 

Hirono, S. and Kollman, P.A. (1991) Relative binding free energy calculations of inhibitors to two mutants (Glu46 — Ala/Gin) of ribonuclease T1 using molecular dynamics/free energy perturbation approaches, Prot. Eng. 4, 233-243. 

Stjernschantz E, Marelius J, Medina C, Jacobsson M, Vermeulen NP, Oosten-brink C. Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization An evaluation of the linear interaction energy (LIE) method. J Chem Inf Model 2006 46 1972-83. 

Wang, J., Deng, Y., and Roux, B. (2006) Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys. J. 91, 2798-2814. 

Miyamoto S and P A Kollman 1993a Absolute and Relative Binding Free Energy Calculations of the Interaction of Biotin and its Analogues with Streptavidin Usmg Molecular Dynamics/Free Energy Perturbation Approaches. Proteins Structure, Function and Genetics 16-226-245. 

Gohlke, H., Kiel, C., Case, D.A. Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes. J. Mol. Biol. 2003,330, 891-913. 

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