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… Yes, using the Rescore solutions tick box in the Fitness & Search Options section under Global Options when using the GOLD Setup GUI. Rescoring, like docking …
… The result of each docking attempt is written out as: gold_soln__m#_n.mol2 where n is the solution number 1,2,3 ... and m# is the number of the ligand, i.e. m1 …
… . The following represents a non-exhaustive list: The ligand crystallographic pose is actually not correct. The ligand file being docked is incorrectly atom- and bond …
… Some third-party programs have difficulty reading files which contain lone pairs. You can choose whether or not lone pairs are included on the docked poses …
… to dock if the binding site is too large or contains functionality that is not matched by equivalent functionality (donor, acceptor or hydrophobic) on the ligand …
… can be created from these docking runs and consensus scores can be created using the arithmetical functionality within GoldMine. Please see the GOLD …
… One simple test of the effectiveness of a docking program is to take a protein-ligand complex from the Protein Data Bank and extract the ligand. The docking …
… function values to suggest accurate binding affinities because many factors are ignored or approximated when calculating a docking score (protein and ligand …
… cores) concurrently. Parallel GOLD dockings are distributed over a PVM at the ligand level such that each ligand is assigned to a particular node within the PVM …
… The main reference for GOLD is: Development and Validation of a Genetic Algorithm for Flexible Docking G. Jones, P. Willett, R. C. Glen, A. R. Leach and R …
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