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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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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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 it not possible to return the crystallographic binding pose of the ligand?
… is a covalently bound ligand. If so, use the option for docking covalent ligands. The binding site definition is either too small or too large with respect to the ligand …
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How do I define my active site?
… containing a list of residues When using a list of residues to define the binding site the file must be in the following format: > HIS69 ARG71 GLU72 ARG127 ASN144 …
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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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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 should I reference SuperStar?
… , 1999 [DOI: 10.1006/jmbi.1999.2809] SuperStar: Improved knowledge-based interaction fields for protein binding sites M. L. Verdonk, J. C. Cole, P. Watson, V. Gillet …
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Can I perform a rigid ligand docking using GOLD?
… Although GOLD was designed to dock flexible ligands into protein binding sites, it is possible to perform a rigid ligand docking. To enable this option, go …
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Does GOLD allow for protein flexibility?
… . The starting positions of Ser, Thr and Tyr OH groups and Lys NH3+ groups therefore do not matter. In cases where you are docking a ligand into a binding site …
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