ArticleProceedings of the National Academy of Sciences of the United States of America2002
On the calculation of absolute macromolecular binding free energies.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
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- Protein dimerization in 2D vs 3D: Geometric allostery enhances binding affinity.The Journal of chemical physics · 2025Article
- Machine Learning Derived Collective Variables for the Study of Protein Homodimerization in Membrane.Journal of chemical theory and computation · 2024Article
- The role of structural heterogeneity in the homodimerization of transmembrane proteins.The Journal of chemical physics · 2023Article
- Multimerizations, Aggregation, and Transfer Reactions of Small Numbers of Molecules.Journal of chemical information and modeling · 2023Article
- On Computing Equilibrium Binding Constants for Protein-Protein Association in Membranes.Journal of chemical theory and computation · 2022Article
- Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach.Journal of chemical theory and computation · 2022Article
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- Energy-entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host-guest challenge.Journal of computer-aided molecular design · 2021Article
- Cavitand Complexes in Aqueous Solution: Collaborative Experimental and Computational Studies of the Wetting, Assembly, and Function of Nanoscopic Bowls in Water.The journal of physical chemistry. B · 2021Review
- Optimal designs for pairwise calculation: An application to free energy perturbation in minimizing prediction variability.Journal of computational chemistry · 2020Article
- Detailed potential of mean force studies on host-guest systems from the SAMPL6 challenge.Journal of computer-aided molecular design · 2018Article
- SAMPL6 host-guest blind predictions using a non equilibrium alchemical approach.Journal of computer-aided molecular design · 2018Article
- Measuring Entropy in Molecular Recognition by Proteins.Annual review of biophysics · 2018Review
- Concentration-Dependent Binding of Small Ligands to Multiple Saturable Sites in Membrane Proteins.Scientific reports · 2017Article
- Entropy in molecular recognition by proteins.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.Proteins · 2015Article
- Efficient Computation of Small-Molecule Configurational Binding Entropy and Free Energy Changes by Ensemble Enumeration.Journal of chemical theory and computation · 2013Article
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2 authors.
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Abstract
The standard framework for calculating the absolute binding free energy of a macromolecular association reaction A + B --> AB with an association constant K(AB) is to equate chemical potentials of the species on the left- and right-hand sides of this reaction and evaluate the chemical potentials from theory. This theory involves (usually hidden) assumptions about what constitutes the bound species, AB, and where the contribution of the solvent appears. We present here an alternative derivation that can be traced back to Bjerrum, in which the expectation value of K(AB) is obtained directly through the statistical mechanical method of evaluating its ensemble (Boltzmann-weighted) average. The generalized Bjerrum approach more clearly delineates: (i) the different contributions to binding; (ii) the origin of the much-discussed and somewhat controversial association entropy term; and (iii) where the solvent contribution appears. This approach also allows approximations required for practical evaluation of the binding constant in complex macromolecular systems, to be introduced in a well defined way. We provide an example, with application to test cases that illustrate a range of binding behavior.
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