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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Which file formats does GOLD support?
… ligand atom types manually. mol (i.e. MDL sd format) Files in mol format may also have the extension .mdl or .sdf. Acceptable input protein file formats are: pdb …
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Why is it not possible to return the crystallographic binding pose of the ligand?
… -typed, or is incorrectly protonated. There are incorrect protein residues. Asn and Gln residues often need to be flipped at the terminal side chain, and His …
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How should I reference Relibase+?
… to reference Relibase/Relibase+ in publications, please use these references: Databases for Protein-Ligand Complexes M. Hendlich, Acta Cryst., D54, 1178-1182, 1998 [DOI …
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Retirement of Relibase/Relibase+
… and allow end users to integrate the searches and information into their own workflows in more flexible ways than Relibase/Relibase+ used to offer. This new …
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Can GOLD be used to dock ligands into DNA or RNA structures?
… . Chem. Inf. Model., 50, 1134–1146, 2010, [DOI: 10.1021/ci9004157]. GOLD was originally designed to handle proteins rather than DNA/RNA. Consequently, GOLD …
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Can I add scatterplots for groups which are not included in the standard IsoStar library?
… restrictions should be noted. IsoGen can only be used to calculate scatterplots from the Cambridge Structural Database (CSD), not from the Protein Data Bank (PDB …
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How should I reference IsoStar?
… . Comput.-Aided Mol. Des., 11, 525-537, 1997 [DOI: 10.1023/A:1007934413448]The Protein Data Bank H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H …
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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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What is CSD-Discovery?
… design including SuperStar intermolecular interaction maps and CSD Full Interaction Maps (FIMS) Protein-ligand docking using GOLD API functions including conformer …
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Where do I deposit data not accepted by the CCDC?
… , www.ccdc.cam.ac.uk/deposit . Data for other compounds are collected by the databases shown below. They can be contacted via their websites for further information. Protein Data …
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