ProtoScore™ is a scoring function for predicting protein-ligand affinity developed as part of the ProtoDiscovery™ suite. It includes calculations for:

  • desolvation of the ligand
  • cation-Pi and sulphur-Pi interactions
  • heterocyclic and aromatic interactions
  • receptor deformation upon binding
  • mismatches between ligand and protein surface
Version 1 of the function was trained on 100 protein complexes and has a Spress value of 5.65kJ/mol with an R² of 0.9. This compares favourably with other commercially available empirical scoring functions.

Version 2 of the function has been trained on a wider range of complexes including a large number of kinases. Pscore_275 was trained on 275 diverse complexes and exhibits and R² of 0.82 with a SD of 6.6kJ/mol whereas Pscore_386 was trained on 386 diverse complexes and exhibits R² of 0.71 with SD of 7.8kJ/mol.

ProtoScore training sets

The ProtoScore™ function operates at the heart of structure based design within ProtoDiscovery™.


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