Linear interaction energy
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How to define energy groups in protein ligand complex (solvated in water) and ligand in water?
Q molecular dynamics package: classical molecular dynamics, linear interaction energy (LIE), linear response approximation (LRA), free energy perturbation (FEP), and empirical valence bond (EVB) simulations.
http://xray.bmc.uu.se/~aqwww/q/
The initial values for alpha and beta in LIE equation are 0.18 and 0.5, respectively. Several groups use iterative LIE approach, i.e. training LIE model to obtain optimal alpha and beta values by using experimental data (e.g. refer to Article Improved Ligand-Protein Binding Affinity Predictions Using M...
The initial LIE values were: alpha = 0.161 and beta = 0.500.
Article A New Method for Predicting Binding Affinity in Computer-Aid...
The refined LIE values, which distinguish beta according to net charge of, and number of hydroxyl groups in, the ligand (or probe in general) are: alpha = 0.18, beta = 0.500 (charged), beta = 0.430 (neutral with no hydroxyl group), beta = 0.37 (neutral with one hydroxyl group), and beta = 0.33 (neutral with two or more hydroxyl groups).Article Ligand binding affinity prediction by linear interaction ene...
Neither alpha nor beta should be considered as a freely adjustable fudge factor. Large deviations from the initial (try first) or refined (see, if you get better results) values suggest a problem with the simulated model rather than with LIE parameters.
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