FAQs
For questions not addressed by a support solution here, please Contact Us. Please do include a description of the problem as well as your operating system and version.
What can we help you with?
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Can GOLD carry out protein-protein docking?
… Most ligand-protein docking programs, including GOLD, are not suitable for docking proteins to other proteins because the problems that must be solved when …
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Is it possible to re-score a given set of GOLD solutions using an alternative scoring function?
… 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 …
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Other than the library size, are there any other major factors that influence the docking time?
… It is not possible to determine how long a ligand or set of ligands will take to dock as this is dependent on, but not limited to, the following: the size …
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Does GOLD allow for protein flexibility?
… GOLD allows for partial protein flexibility in all dockings. Specifically GOLD rotates the torsion angles of serine, threonine and tyrosine hydroxyl groups …
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Is it possible to perform blind docking using GOLD?
… docking experiments on all of these. …
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Why do I get different fitness scores for consecutive dockings with the same input files?
… Consecutive dockings using the same input files will not give identical solutions or fitness scores. The reason for this is fundamental to the way in which …
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Can GOLD be used to dock ligands into DNA or RNA structures?
… GOLD can be used to dock ligands to DNA and RNA structures, however it has not been specifically parametrised to handle these and extensive validation work has …
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Can I perform a rigid ligand docking using GOLD?
… Although GOLD was designed to dock flexible ligands into protein binding sites, it is possible to perform a rigid ligand docking. To enable this option, go …
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What is the naming convention for ligand output files?
… 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 …
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Can I reduce the amount of output produced by GOLD?
… with the best fitness score. For the docking of ultra-large libraries, it is recommended to use the MIN_OUT write option, which will return only the bestranking.lst …
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