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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Why is there a discrepancy between the final fitness score and the calculated fitness score (from individual terms) of a docking performed using the GOLD API?
… Under some circumstances when using the GOLD API there may be a discrepancy between the calculated fitness score and the final fitness score displayed …
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What is the z-score listed in the summary statistics for each 3D bond and valence angle search result?
… The z-score is the absolute difference between observed and mean values of a geometric parameter divided by the standard deviation of the Mogul distribution …
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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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What is the difference between the GoldScore, ChemScore, ASP and ChemPLP scoring functions provided with GOLD?
… The GoldScore, ChemScore, ASP (the Astex Statistical Potential) and ChemPLP fitness scores are dimensionless. However in each case the scale of the score gives …
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How do I use GOLD to predict binding affinity?
… GOLD has been optimised for the prediction of ligand binding positions rather than the prediction of binding affinities. It is not recommended to use scoring …
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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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Why do I get different fitness scores for consecutive dockings with the same input files?
… Consecutive dockings using the same input files will not give identical solutions or fitness scores. The reason for this is fundamental to the way in which …
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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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