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. 2018 Oct 22;9:1038. doi: 10.3389/fphar.2018.01038

Table 2.

Comparative evaluation of protein-ligand (fungicide) docking interactions from YASARA programme and XP Glide score (docking score) values.

S. No. Fungicide YASARA score Dissociation constant (Kd) (μM) XPG score (kcal/mol) MM/GBSA (ΔGbind) (kcal/mol)
1. Oxathiapiprolin 7.81 1.86 −1.89 ± 0.32 −75.50 ± 0.54
2. Famoxadone 7.65 2.43 −3.30 ± 0.28 −66.90 ± 0.47
3. Metiram 4.10 976.17 −6.13 ± 0.25 −55.63 ± 0.38
4. Dithane 4.10 976.17 −6.13 ± 0.22 −55.63 ± 0.42
5. Pterostilbin 6.29 24.17 −4.30 ± 0.20 −50.69 ± 0.56
6. Tolclofos-methyl 4.91 249.18 1.38 ± 0.10 −40.70 ± 0.47
7. Fluberidazole 6.63 13.64 −1.79 ± 0.33 −37.50 ± 0.52
8. Tolprocarb 6.64 13.50 −4.55 ± 0.64 −35.02 ± 0.64
9. Cymoxanil 5.70 57.90 −3.35 ± 0.24 −33.39 ± 0.76
10. Carbendazim 5.78 57.09 −2.98 ± 0.38 −32.28 ± 0.49
11. Coumarin 6.13 32.05 −1.19 ± 0.19 −14.58 ± 0.36
12. Pyraclostrobin 7.05 6.69 −7.02 ± 0.10 −14.57 ± 0.39
13. Triazoquinoline 6.43 19.25 −0.45 ± 0.30 −13.19 ± 0.33
14. Fludioxonil 5.98 40.87 −3.53 ± 0.24 −8.07 ± 0.13
15. Iprodione 5.98 41.08 −4.42 ± 0.34 −3.30 ± 0.31
16. Ethyl phosphonate 5.05 197.07 −4.78 ± 0.25 −2.14 ± 0.51
17. Prothioconazole 5.53 87.65 1.64 ± 0.11 8.94 ± 0.43
18. Benomyl 5.58 80.15 2.53 ± 0.39 29.98 ± 0.74
19. Prochloraz 5.43 103.25 5.68 ± 0.36 43.86 ± 0.80

The YASARA based dissociation constant (Kd) have been given in a separate column. The docked complexes were further rescored for binding free energy assessment using the MM/GBSA method. The MM/GBSA based binding free energies have been arranged in the increasing order, reflects the decreasing order of stability and steadiness of the complexes. The Glide based interaction of the protein-fungicide docking complexes and binding free energy assessment through MM/GBSA were set up with three replication and data were analyzed by Mean (± SE) was calculated from three replicates for each of the docked complexes. We have shown the docking score values only for the significant docked protein-ligand complexes (19 fungicides; as others were found unable to dock at the intended site through Glide XP dock and also had positive free energies as calculated through MM/GBSA approach.