ArticleScientific reports2022
A highly accurate metadynamics-based Dissociation Free Energy method to calculate protein-protein and protein-ligand binding potencies.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
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- MnM-W-MMGBSA: A Computational Strategy to Improve Relative Binding Free Energies of Protein-Protein Interaction Systems.The journal of physical chemistry. B · 2025Article
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- In Vitro and In Vivo Effects of Resveratrol on Rat Hepatic CYP1A2.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Discovery of a potent ROR1 inhibitor using μs-scale MD simulations, wt-metadynamics, and absolute binding free energy calculations.Journal of molecular modeling · 2025Article
- Charge distribution and helicity tune the binding of septin's amphipathic helix domain to membranes.Biophysical journal · 2025Article
- From Apo to Ligand-Bound: Unraveling PPARγ-LBD Conformational Shifts via Advanced Molecular Dynamics.ACS omega · 2025Article
- Quantum Mechanics-Based Ranking of Predicted Proteolysis Targeting Chimeras-Mediated Ternary Complexes.ACS medicinal chemistry letters · 2025Article
- Estimating Absolute Protein-Protein Binding Free Energies by a Super Learner Model.Journal of chemical information and modeling · 2025Article
- ModBind, a Rapid Simulation-Based Predictor of Ligand Binding and Off-Rates.Journal of chemical information and modeling · 2025Article
- Insights into the role of dynamical features in protein complex formation: The case of SARS-CoV-2 spike binding with ACE2.Computational and structural biotechnology journal · 2025Article
- Targeting fusion oncoproteins in childhood cancers: challenges and future opportunities for developing therapeutics.Journal of the National Cancer Institute · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
- Molecular Dynamics Simulations in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- De Novo Design of Anti-COVID Drugs Using Machine Learning-Based Equivariant Diffusion Model Targeting the Spike Protein.Current issues in molecular biology · 2023Article
- Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction.RSC chemical biology · 2023Review
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5 authors.
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Abstract
Although seeking to develop a general and accurate binding free energy calculation method for protein-protein and protein-ligand interactions has been a continuous effort for decades, only limited successes have been obtained so far. Here, we report the development of a metadynamics-based procedure that calculates Dissociation Free Energy (DFE) and its application to 19 non-congeneric protein-protein complexes and hundreds of protein-ligand complexes covering eight targets. We achieved very high correlations in comparison to experimental binding free energies for these diverse sets of systems, demonstrating the generality and accuracy of the method. Since structures of most proteins are available owing to the recent success of prediction by artificial intelligence, a general free energy method such as DFE, combined with other methods, can make structure-based drug design a widely viable and reliable solution to develop both traditional small molecule drugs and biologic drugs as well as PROTACS.
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