The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

Figures & data

Figure 1. The number of hits per year in Web of Science when searching for the topics MM/PBSA, MM-PBSA, MM/GBSA or MM-GBSA.

Table 1. The various MM/PBSA terms (cf. Equation 55 ) for the binding of seven biotin analogues to avidin (kJ/mol).

Term	Btn1	Btn2	Btn3	Btn4	Btn5	Btn6	Btn7	SD1	SD7
Eel	–1224	–1295	–1287	–174	–83	–50	–109	46	21
EvdW	–148	–149	–132	–200	–128	–128	–49	16	11
Gpol	1224	1321	1259	266	146	123	124	30	13
Gnp	–17	–17	–17	–21	–16	–16	–11	0	0
TS	–81	–96	–70	–82	–67	–66	–28	46	57
Eel + Gpol	0	26	–27	92	63	72	15	22	20
ΔGbind	–187	–145	–222	–114	–49	–34	–53	47	62

The two last columns (SD1 and SD7) show the standard deviation of the various terms for Btn1 and Btn7. Ligands Btn1–Btn3 have a net charge of –1, whereas the other four ligands are neutral.

Adapted with permission from [29] (the 03oh/03 calculation with PB solvation). Copyright (2006) American Chemical Society.

Figure 2. Dependence of the MM/PBSA results on the continuum-solvation model for the binding of seven biotin analogues to avidin.

Weis A, Katebzadeh K, Söderhjelm P, et al. Ligand affinities predicted with the MM/PBSA method:  Dependence on the simulation method and the force field. J Med Chem 2006;49:6596-606

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Genheden S, Luchko T, Gusarov S, et al. An MM/3D-RISM approach for ligand-binding affinities. J Phys Chem B 2010;114:8505-16

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