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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How do I use GOLD to predict binding affinity?
… GOLD has been optimised for the prediction of ligand binding positions rather than the prediction of binding affinities. It is not recommended to use scoring …
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What is the difference between the GoldScore, ChemScore, ASP and ChemPLP scoring functions provided with GOLD?
… function incorporates a term, dG, that represents the total free energy change that occurs on ligand binding and was trained by regression against binding affinity …
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Why do I get different fitness scores for consecutive dockings with the same input files?
… of protein ligand interactions. Each chromosome is assigned a fitness score based on its predicted binding affinity and the chromosomes within the population …
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Is it possible to perform blind docking using GOLD?
… Unfortunately GOLD is not ideally suited to cases where no binding site is to be designated. GOLD currently has a built-in upper limit on the maximum size …
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Can GOLD carry out protein-protein docking?
… docking proteins are sufficiently different from those when docking ligands. In particular GOLD requires a distinct concave binding site to be defined, whereas …
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Why is it not possible to return the crystallographic binding pose of the ligand?
… crystallographic binding pose can be reproduced better. The GOLD docking algorithm returns only very similar binding poses. If so, try using the Diverse …
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Other than the library size, are there any other major factors that influence the docking time?
… of the defined binding site the size and flexibility of the ligand(s) the computer speed the GOLD configuration (e.g. docking runs that allow for flexible side …
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Why is GOLD unable to dock a particular ligand?
… 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 …
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How do the default settings for GOLD differ in the MOE interface compared to standalone GOLD?
… The default set up in the GOLD interface in CCG's MOE is designed to generate a variety of plausible and different binding poses. There are some differences …
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Is it possible to re-score a given set of GOLD solutions using an alternative scoring function?
… , requires a prepared protein input file and a fully defined binding site (preferably the same definition that was used for the original docking). The ligand(s …
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