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 know whether to flip or rotate Ring-NHR, Ring-NR1R2 and protonated carboxylic acids when setting ligand flexibility?
… When setting ligand flexibility, by default, all planar Ring-NHR, Ring-NR1R2 and carboxylic acids are set to 'Flip' i.e. to rotate through 180 degrees only …
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What is CSD-Core?
… data. Capabilities of CSD-Core include: Powerful search, advanced 2D/3D visualisation and flexible results analysis Conformation analysis Fragment interaction …
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How should I reference SuperStar?
… SuperStar: A knowledge-based approach for identifying interaction sites in proteins M. L. Verdonk, J. C. Cole and R. Taylor, J. Mol. Biol., 289, 1093-1108 …
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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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GOLD fails to recognise the metal in my metal-containing enzyme
… GOLD has parameters for a number of metals found in proteins but only the following metals are included: Mg, Zn, Mn, Fe, Ca, Co, Gd, Cu, Hg, Cd, Ni and V …
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Which scoring function is best for general use?
… prediction and virtual screening, and thus it is now the default scoring function in GOLD. Other scoring functions may work well for certain protein targets. ChemScore …
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Why are my H-bond constraints not being taken into account?
… A ligand atom may be constrained to form a hydrogen bond to a particular protein atom. One atom should be a hydrogen atom on a H-bond donor and the other …
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Is it possible to perform blind docking using GOLD?
… of a binding site which is 20Å from a specified point or ligand. The only approach is to split the protein into multiple binding sites and carry out individual …
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How do the default settings for GOLD differ in the MOE interface compared to standalone GOLD?
… from the default settings used in GOLD. These are (MOE v.s. standalone GOLD): Number of GA runs: 30 v.s. 10 Diverse Solutions: on v.s. off Flexible ligand ring …
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Does GOLD calculate or use atomic charges?
… with the atom's normal valency. For this reason, it is essential that the bond and atom types are set up correctly for both the protein and the ligand …
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