ArticleMethods in molecular biology (Clifton, N.J.)2022
Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria.
Article in Methods in molecular biology (Clifton, N.J.), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed.
- Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer Method with Coordinate Swapping.Journal of chemical information and modeling · 2025Article
- Potential distribution theory of alchemical transfer.The Journal of chemical physics · 2025Article
- What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling.Journal of chemical theory and computation · 2024Article
- Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.Physical chemistry chemical physics : PCCP · 2022Article
- Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge.Journal of computer-aided molecular design · 2022Article
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Abstract
This chapter discusses the theory and application of physics-based free energy methods to estimate protein-peptide binding free energies. It presents a statistical mechanics formulation of molecular binding, which is then specialized in three methodologies: (1) alchemical absolute binding free energy estimation with implicit solvation, (2) alchemical relative binding free energy estimation with explicit solvation, and (3) potential of mean force binding free energy estimation. Case studies of protein-peptide binding application taken from the recent literature are discussed for each method.
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