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 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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How do I remove lone pairs from GOLD docking solutions?
… 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 …
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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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Can I reduce the amount of output produced by GOLD?
… and gold.log file for each docking. All other files (including the GOLD docking poses) will not be written out. …
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Why is GOLD unable to dock a particular ligand?
… . This is because GOLD requires at least three matches of complementary fitting points between protein and ligand before a binding pose can be scored. Where …
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How should I reference SuperStar?
… for the prediction of protein-ligand interactions D. R. Boer, J. Kroon, J. C. Cole, B. Smith and M. L. Verdonk, J. Mol. Biol., 312, 275-287, 2001 [DOI …
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How should I reference CSD-Particle?
… For VisualHabit functionality the reference is HABIT - a program for predicting the morphology of molecular crystalsG. Clydesdale, R. Docherty, K. J. Roberts …
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Can GOLD handle metals?
… protein atoms or water molecules in the original file so that GOLD can predict the coordination geometry. When the protein input file is prepared, the metal ion …
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What is the naming convention for ligand output files?
… for the first ligand, m2 for the second, etc. Please note that the file gold_soln__m1_1.mol2 is not necessarily the best GOLD prediction, it is only …
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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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