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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Does GOLD allow for protein flexibility?
… GOLD allows for partial protein flexibility in all dockings. Specifically GOLD rotates the torsion angles of serine, threonine and tyrosine hydroxyl groups …
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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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How should I reference GOLD?
… The main reference for GOLD is: Development and Validation of a Genetic Algorithm for Flexible Docking G. Jones, P. Willett, R. C. Glen, A. R. Leach and R …
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What is the difference between the GoldScore, ChemScore, ASP and ChemPLP scoring functions provided with GOLD?
… data for 82 complexes. The ChemScore fitness function also incorporates a protein-ligand atom clash term and an internal energy term. ChemScore takes account …
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Can GOLD carry out protein-protein docking?
… Most ligand-protein docking programs, including GOLD, are not suitable for docking proteins to other proteins because the problems that must be solved when …
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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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Has GOLD been validated?
… One simple test of the effectiveness of a docking program is to take a protein-ligand complex from the Protein Data Bank and extract the ligand. The docking …
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How can I view only the ligand and surrounding residues rather than the whole protein-ligand complex?
… Having loaded a protein-ligand complex in Hermes, you need to define how large you want your complex to look. To do so, right-click in Hermes and navigate …
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Why is GOLD unable to dock a particular ligand?
… The vast majority of problems of this nature are caused by incorrectly set up ligand and/or protein input files. GOLD uses an all atom model, so the protein …
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How do I remove lone pairs from GOLD docking solutions?
… cannot choose whether or not lone pairs are included on the protein: when GOLD writes this protein file out, it will contain any lone pairs for atoms …
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