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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If I apply a distance or a scaffold constraint, will it always be obeyed?
… No, it will not always be obeyed. If a distance constraint or a scaffold constraint is applied, then a harmonic penalty term is added to the scoring function …
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Why is it not possible to return the crystallographic binding pose of the ligand?
… microenvironments in the active site. The scoring function used is not the best for the protein in question. If so, try another scoring function to see if the ligand …
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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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Has GOLD been validated?
… in the following publication: "Pose prediction and virtual screening performance of GOLD scoring functions in a standardized test.", J. W. Liebeschuetz, et al., JCAMD …
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What are the strengths/weaknesses of similarity searching in WebCSD?
… fewer atoms will also be less well defined, and therefore are more prone to low similarity scores. Finally, no information is stored about chemically related …
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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 …