Protein-ligand binding affinities

D. A. Annis, N. Nazef, C.-C. Chuang, M. P. Scott, H. M. Nash A general technique to rank protein—ligand binding affinities and determine allosteric versus direct binding site competition in compound mixtures. 

The protein-ligand binding affinity is usually expressed as the equilibrium dissociation constant, K, which is described by the following relationship between the concentrations of free receptor [ ], free ligand [S], and the receptor-ligand complex [ES ... 

Scott MP, Nash HM A general technique to rank protein-ligand binding affinities and determine allosteric versus direct binding site... 

Gilson, M. K., and Zhou, H. X. (2007). Calculation of protein-ligand binding affinities. Annu. Rev. Biophys. Biomol. Struct. 36, 21—42. 

Learning Methods and annotated databases of protein-ligand binding affinity and... 

T. Liu, Y. Lin, X. Wen, R. N. Jorissen and M. K. Gilson, BindingDB a web-accessible database of experimentally determined protein-ligand binding affinities., Nucleic Acids Res., 2007, 35, D198-D201. 

Smithrud DB, Wyman TB, Diederich E. Enthalpically driven cyclophane arene inclusion complexation - Solvent-dependent calorimetric studies. J. Am. Chem. Soc. 1991 113 5420-5426. Gilson MK, Zhou HX. Calculation of protein-ligand binding affinities. Annu. Rev. Biophys. Biomol. Struct. 2007 36 21 2. Karplus M, McCammon JA. Molecular dynamics simulations of biomolecules. Nat Struct Biol 2002 9 646-652. 

Terp GE, Johansen BN, Christensen IT, Jorgensen FS. A new concept for multidimensional selection of ligand conformations (multiselect) and multidimensional scoring (multiscore) of protein-ligand binding affinities. J Med Chem 2001 44 2333 13. 

Lee, M. S., and Olson, M. A. (2006) Calculation of absolute protein-ligand binding affinity using path and endpoint approaches. Biophys. J. 90, 864-877. 

Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA. 

Force fields were originally developed to simulate the conformational, thermodynamic and kinetic behaviors of small molecules or macromolecules much more efficiently, from a computer resource perspective, than quantum mechanical methods. It was hoped that if the interaction components of the force fields were applied to docking and scoring, the more accurate representation of the physics of protein ligand interactions would result in more accurate predictions of protein ligand binding affinities. 

Br. . . It interactions as an important contribution to protein-ligand binding affinity. Angewandte Chemie, 121, 2955-2960. 

A New Concept for Multidimensional Selection of Ligand Conformations (Multiselect) and Multidimensional Scoring (Multiscore) of Protein-Ligand Binding Affinities. 

Callicchio, E., 8c Levy, R. M. (2011). Advances in all atom sampling methods for modeling protein-ligand binding affinities. Current Opinion in Structural Biology, 161,161-166. 

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