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 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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Does GOLD allow for protein flexibility?
… during docking in order to optimise hydrogen bonding interactions of these residues with the ligand. The positions of lysine NH3+ groups are similarly optimised …
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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 can I calculate a score per binding site residue?
… in the box labelled "Save per atom scores". To aggregate these scores on a per residue basis you will need to create a GoldMine from your docking results. See …
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What data can I download from the CCDC?
… The CSD also includes peptides and saccharides of up to 24 residues and mono-, di- and tri-nucleotides. Thanks to a new collaboration between the CCDC and FIZ …
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How can I view only the ligand and surrounding residues rather than the whole protein-ligand complex?
… How can I view only the ligand and surrounding residues rather than the whole protein-ligand complex? …
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What are the criteria for deposition to the CCDC?
… and saccharides of up to 24 residues; higher oligomers are covered by the Protein Data Bank The CSD covers mono-, di- and tri-nucleotides; higher oligomers …
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