Mean-force scoring function

Mean-Force Scoring Functions for Protein-Ligand Binding... 

Since the reference state is inaccessible for protein systems, the calculations for p in Eq. (5) could be arbitrary in real applications. Therefore, a challenging task in the derivation of mean-force scoring functions is how to calculate p j r) of... 

MEAN-FORCE SCORING FUNCTIONS FOR PROTEIN-LIGAND DOCKING... 

The mean-force scoring functions based upon an atom-randomized reference state use the method for the simple monatomic system to calculate p (r). In this method, it is assumed that all the atoms are randomly placed in the system without interatomic interactions, ignoring interatomic connectivity, excluded volume, and other factors in the structures of protein-ligand complexes. The resulted pair potentials w,y are then taken as the true potentials Uy despite their differences, and the binding energy score is calculated as... 

DeWitte and Shakhnovich developed a mean-force scoring function (SMoG) for de novo lead design using 13 protein and 13 ligand atom types [59]. It was based on a set of contact-based potentials in which a ligand atom is defined as in contact with a protein atom if they are within 5 A from each other. The potential parameter wy was derived from the statistical information about interatomic interactions in crystal structures as... 

Gohlke et al. developed a mean-force scoring function (DrugScorePDB) based on 17 atom types and 1376 protein-ligand complex structures from the PDB [52]. In their method, they also followed Sippl s formalism [39] to calculate the pair potentials ... 

Other examples of mean-force scoring functions based on the atom-randomized reference state include MScore [63], ASP [64], KScore [57], etc. 

In this chapter, we have reviewed the current types of mean-force scoring functions according to how they treat the reference state. Despite considerable progress, several lines remain open for future development. First, as demonstrated and discussed in our previous study [48], explicit inclusion of the entropic effects may significantly improve the accuracy of a mean-force scoring function. Second, the appropriate categorization of atom types with a good balance of the statistics... 

Huang S-Y, Zou X (2010) Mean-force scoring functions for protein-ligand binding. Aram Rep Comput Chem 6 281-296... 

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