Solution

The GoldScore, ChemScore, ASP (the Astex Statistical Potential) and ChemPLP fitness scores are dimensionless. However in each case the scale of the score gives 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 function provided with GOLD, and is the one selected by default for GOLD versions 5.0 and earlier. It has been optimised for the prediction of ligand binding positions and takes into account factors such as H-bonding energy, van der Waals energy, metal interaction and ligand torsion strain.

The ChemScore fitness function incorporates a term, dG, that represents the total free energy change that occurs on ligand binding and was trained by regression against binding affinity data for 82 complexes. The ChemScore fitness function also incorporates a protein-ligand atom clash term and an internal energy term. ChemScore takes account of hydrophobic-hydrophobic contact area, hydrogen bonding, ligand flexibility and metal interaction. Although partly derived using binding affinity data, ChemScore values should not be used explicitly as values for binding energy or binding affinity.

The ASP fitness function is an atom-atom distance potential derived from a database of protein-ligand complexes and can be compared to other knowledge-based scoring potentials, e.g. PMF and DrugScore. ASP incorporates some ChemScore terms.

ChemPLP uses the ChemScore hydrogen bonding term and multiple linear potentials to model van der Waals and repulsive terms. It is fast to calculate (slightly faster than ChemScore and 4x faster than GoldScore) and recent validation tests have shown it to be generally more effective than the other scoring functions for both pose prediction and virtual screening. This scoring function is the default for GOLD version 5.1 and later.


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