The Performance of Several Docking Programs at Reproducing Protein–Macrolide-Like Crystal Structures

Abstract

The accuracy of five docking programs at reproducing crystallographic structures of complexes of 8 macrolides and 12 related macrocyclic structures, all with their corresponding receptors, was evaluated. Self-docking calculations indicated excellent performance in all cases (mean RMSD values ≤ 1.0) and confirmed the speed of AutoDock Vina. Afterwards, the lowest-energy conformer of each molecule and all the conformers lying 0–10 kcal/mol above it (as given by Macrocycle, from MacroModel 10.0) were subjected to standard docking calculations. While each docking method has its own merits, the observed speed of the programs was as follows: Glide 6.6 > AutoDock Vina 1.1.2 > DOCK 6.5 >> AutoDock 4.2.6 > AutoDock 3.0.5. For most of the complexes, the five methods predicted quite correct poses of ligands at the binding sites, but the lower RMSD values for the poses of highest affinity were in the order: Glide 6.6 ≈ AutoDock Vina ≈ DOCK 6.5 > AutoDock 4.2.6 >> AutoDock 3.0.5. By choosing the poses closest to the crystal structure the order was: AutoDock Vina > Glide 6.6 ≈ DOCK 6.5 ≥ AutoDock 4.2.6 >> AutoDock 3.0.5. Re-scoring (AutoDock 4.2.6//AutoDock Vina, Amber Score and MM-GBSA) improved the agreement between the calculated and experimental data. For all intents and purposes, these three methods are equally reliable.

In silico study of anthocyanin and ternatin flavonoids for the treatment of inflammation-related diseases using molecular docking analysis

“…Structure-based docking methods rank molecules via a scoring function that is calculated based on their inner methods (Yang et al, 2019). In addition, the previous study also showed that AutoDock Vina was a more efficient option for stimulating protein docking with macrolides and analogues of intermediate size ligand compared to other docking programs, such as Glide 6.6, AutoDock 4.2 and DOCK 6.5 (Castro-Alvarez et al, 2017).…”

Genetic algorithm with a crossover elitist preservation mechanism for protein–ligand docking

“…A docked conformation with a smaller RMSD is considered as a more accurate solution to the docking problem. Compared CEPGA with GA, LGA, SODOCK, and ABC (Castro-Alvarez et al 2017 ; Feinstein and Brylinski 2015 ), Table 2 show that CEPGA has the best performance in the search for the lowest energy and the smallest RMSD of molecular docking conformations.…”

Biological Evaluation and Molecular Docking Studies of Benzalkonium Ibuprofenate

“…Glide offers the full range of speed vs. accuracy options, from the HTVS (high-throughput virtual screening) mode for efficiently enriching million compound libraries, to the SP (standard precision) mode for reliably docking tens to hundreds of thousands of ligand with high accuracy, and to the extra precision (XP) mode where further elimination of false positives is accomplished by more extensive sampling and advanced scoring, resulting in even higher enrichment. Many researchers carried out extensive comparisons of several docking programs and scoring functions using an extensive data set of pharmaceutically attractive targets and active compounds [13][14][15][16][17][18]. All the study leads to the same result that Glide XP methodology was shown to yield enrichments superior to the alternative methods consistently.…”