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 can I run GOLD in parallel?
… GOLD docking on a workstation. However, the setup involved isn't trivial and might not be straightforward on all platforms. A simpler solution for this use-case …
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Why is it not possible to return the crystallographic binding pose of the ligand?
… . The following represents a non-exhaustive list: The ligand crystallographic pose is actually not correct. The ligand file being docked is incorrectly atom- and bond …
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How do I remove lone pairs from GOLD docking solutions?
… Some third-party programs have difficulty reading files which contain lone pairs. You can choose whether or not lone pairs are included on the docked poses …
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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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Does GOLD calculate or use atomic charges?
… . For further information, please refer to the GOLD documentation. Formal charges will be output to the saved protein.mol2 file and to the GOLD docking poses. …
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Is it possible to carry out consensus scoring with GOLD?
… can be created from these docking runs and consensus scores can be created using the arithmetical functionality within GoldMine. Please see the GOLD …
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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 calculate a score per binding site residue?
… It is possible to save scores on a per atom basis whilst docking with GOLD. This can be done by setting the 'per_atom_scores' keyword in the GOLD configuration …
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How do I use GOLD to predict binding affinity?
… function values to suggest accurate binding affinities because many factors are ignored or approximated when calculating a docking score (protein and ligand …
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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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