BLEEP potential

Mitchell, J. B. O., Laskowski, R. A., Alex, A., and Thornton, J. M. (1999) BLEEP-potential of mean force describing protein-ligand interactions I. Generating potential.. /. Comp. Chem. 20, 1165-1176. 

BLEEP—Potential of Mean Force Describing Protein—Ligand Interactions. I. Generating Potential. 

Chem., 20, 1177 (1999). BLEEP-Potential of Mean Force Describing Protein-Ligand Interactions. II. Calculation of Binding Energies and Comparison with Experimental Data. 

J. B. O. Mitchell, R. A. Laskowski, A. Alex, M. J. Forster and J. M. Thornton, BLEEP-Potential of mean force describing protein-ligand interactions II. Calculation of binding energies and comparison with experimental data.. Journal of Computational Chemistry, 1999, 20, 1177-1185. 

Mitchell and coworkers choose a different type of reference state for their BLEEP potential (315). The pair interaction energy is written as... 

Mitchell JBO, Laskowski RA, Alex A, Thornton JM. BLEEP-potential of mean force... 

Alex, A., and Thornton, J.M. BLEEP -A potential of mean force describing protein-ligand interactions I. 

Besides differences in the functional form and reference state, from a more practical point of view, the knowledge-based potentials differ also with respect to scope of atom type definitions and the amount of structural data used for their derivation. The number of different atom types ranges from 17 in Drug-Score to 40 nonmetal atom types in BLEEP. In all cases, the Protein Data Bank (321) was the source of the solved crystal structures. For BEEEP 351 selected complexes were used, whereas the PMF function was extracted from 697 complexes, and DrugScore was derived using 1376 complexes. In the latter case, the data have been extracted from Relibase (322,323). 

Mitchell et al. developed an atomic-level potential of mean force for protein-ligand interactions (BLEEP) based on two hydrogen types, 38 nonmetal heavy atom types, and 18 metal types [54]. The mean-force potential between atom types i and / at interatomic distance r was also derived based on Sippl s sparse data correction method [39]... 

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