ReviewAdvances in protein chemistry and structural biology2011
Recent theoretical and computational advances for modeling protein-ligand binding affinities.
Review in Advances in protein chemistry and structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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69 citing papers in PubMed.
- Toward Reconciling the Standard Binding Free Energy of Lenacapavir to HIV-1 Capsid with Experiment: Thermodynamic Effects of Solvent Buffer and Ligand Reorganization.The journal of physical chemistry. B · 2026Article
- Automated On-the-Fly Optimization of Resource Allocation for Efficient Free Energy Simulations.Journal of chemical information and modeling · 2025Article
- Applying Absolute Free Energy Perturbation Molecular Dynamics to Diffusively Binding Ligands.Journal of chemical theory and computation · 2025Article
- 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
- Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation.Journal of chemical information and modeling · 2025Article
- Potential distribution theory of alchemical transfer.The Journal of chemical physics · 2025Article
- Binding Selectivity Analysis from Alchemical Receptor Hopping and Swapping Free Energy Calculations.The journal of physical chemistry. B · 2024Article
- Incorporating Prior Knowledge in the Seeds of Adaptive Sampling Molecular Dynamics Simulations of Ligand Transport in Enzymes with Buried Active Sites.Journal of chemical theory and computation · 2024Article
- On Analytical Corrections for Restraints in Absolute Binding Free Energy Calculations.Journal of chemical information and modeling · 2024Article
- PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model.Journal of chemical theory and computation · 2024Article
- 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
- Article
- Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization.bioRxiv : the preprint server for biology · 2023Article
- A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model.The Journal of chemical physics · 2023Article
- Comparison of Receptor-Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations.Journal of chemical theory and computation · 2023Article
- Discovery of the allosteric inhibitor from actinomyces metabolites to target EGFRScientific reports · 2023Article
- A proteomics-MM/PBSA dual approach for the analysis of SARS-CoV-2 main protease substrate peptide specificity.Peptides · 2022Article
- High Order Ab Initio Valence Force Field with Chemical Pattern Based Parameter Assignment.Journal of computational biophysics and chemistry · 2022Article
- Drug Design by Pharmacophore and Virtual Screening Approach.Pharmaceuticals (Basel, Switzerland) · 2022Review
- 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
9 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
We review recent theoretical and algorithmic advances for the modeling of protein ligand binding free energies. We first describe a statistical mechanics theory of noncovalent association, with particular focus on deriving the fundamental formulas on which computational methods are based. The second part reviews the main computational models and algorithms in current use or development, pointing out the relations with each other and with the theory developed in the first part. Particular emphasis is given to the modeling of conformational reorganization and entropic effect. The methods reviewed are free energy perturbation, double decoupling, the Binding Energy Distribution Analysis Method, the potential of mean force method, mining minima and MM/PBSA. These models have different features and limitations, and their ranges of applicability vary correspondingly. Yet their origins can all be traced back to a single fundamental theory.
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