Performance evaluation of docking programs- Glide, GOLD, AutoDock & SurflexDock, using free energy perturbation reference data: A case study of fructose-1, 6-bisphosphatase-AMP analogs.

Performance evaluation of docking programs- Glide, GOLD, AutoDock & SurflexDock, using free energy perturbation reference data: A case study of fructose-1, 6-bisphosphatase-AMP analogs.
Mini Rev Med Chem. 2020 May 26;:
Authors: Reddy KK, Rathore RS, Srujana P, Burri RR, Reddy CR, Sumakanth M, Reddanna P, Reddy MR
Abstract
The accurate ranking of analogs of lead molecules with respect to their estimated binding free energies to drug targets remains highly challenging in molecular docking due to small relative differences in their free energy values. Free energy perturbation (FEP) method, which provides the most accurate relative binding free energy values was earlier used to calculate free energies of many ligands for several important drug targets including Fructose-1,6-BisphosPhatase (FBPase). The availability of abundant structural and experimental binding affinity data for FBPase inhibitors provided an ideal system to evaluate four widely used docking programs, AutoDock, Glide, GOLD and SurflexDock, distinct from earlier comparative evaluation studies. The analyses suggested that, considering various parameters such as docking pose, scoring and ranking accuracy, sensitivity analysis and newly introduced relative ranking score, Glide provided the most consistent results in all respects for the system studied in the present work. Whereas GOLD and AutoDock.also demonstrated better performance, AutoDock results were found to be si...

Source: Mini Reviews in Medicinal Chemistry - May 25, 2020 Category: Chemistry Authors: Reddy KK, Rathore RS, Srujana P, Burri RR, Reddy CR, Sumakanth M, Reddanna P, Reddy MR Tags: Mini Rev Med Chem Source Type: research