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 scoring function is best for general use?
… All the scoring functions have strengths and weaknesses. We have found that ChemPLP on the whole is the best performing scoring function for both pose …
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Is it possible to carry out consensus scoring with GOLD?
… It is possible to rescore poses generated by GOLD with any of five scoring functions (GoldScore, ASP, ChemScore, ChemScore RDS and ChemPLP). GoldMine databases …
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Can I modify the scoring functions in GOLD?
… During a docking run GOLD scores solutions according to a fitness function. GOLD offers a choice of fitness functions for scoring: GoldScore, ChemScore, ASP …
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What is the difference between the GoldScore, ChemScore, ASP and ChemPLP scoring functions provided with GOLD?
… a guide as to how good the pose is; the higher the score, the better the docking result is likely to be. The GoldScore fitness function is the original scoring …
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If I apply a distance or a scaffold constraint, will it always be obeyed?
… No, it will not always be obeyed. If a distance constraint or a scaffold constraint is applied, then a harmonic penalty term is added to the scoring function …
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Is it possible to re-score a given set of GOLD solutions using an alternative scoring function?
… ) file(s), scoring function and output preferences must also all be specified. It is possible to rescore both GOLD docking poses & docking poses from other docking …
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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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Why is GOLD unable to dock a particular ligand?
… types; SYBYL bond types are also used. The correct assignment of atom and bond types is crucial for GOLD to function correctly. Ligands will sometimes fail …
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Why is it not possible to return the crystallographic binding pose of the ligand?
… microenvironments in the active site. The scoring function used is not the best for the protein in question. If so, try another scoring function to see if the ligand …
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Can I reduce the amount of output produced by GOLD?
… fitness function rankings and/or ligand log files and/or initialised ligand files. It is also possible to filter output according to fitness by: rejecting …
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