Design of scoring functions
This page is for general guidelines on designing scoring functions.
Some guidelines:
Representation invariance: The score of a given configuration should not change dramatically if the number of particles used to represent the model changes. That is, representing a protein with all atoms or one particle per residue should result in the same score (up to errors introduced by the coarsened representation).
Specificity invariance: increasing the specificity of the restraint shouldn't change the score of good solutions. For example, replacing a fit restraint on an assembly of two proteins with two, aligned fit restraints for the components should not change the scores when the components are in the proper location.