ArticleJournal of chemical theory and computation2020
Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies.
Article in Journal of chemical theory and computation, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 44 citations in OpenAlex.
- Investigating whether deep learning models for co-folding learn the physics of protein-ligand interactions.Nature communications · 2025Article
- Efficacy of Combined PD-1 Inhibitor and Bevacizumab in Unresectable Liver Metastasis of MSI-H Colorectal Cancer: A Case Report.The American journal of case reports · 2025Article
- Host-Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol.Journal of chemical theory and computation · 2024Article
- Absolute Binding Free Energies with OneOPES.The journal of physical chemistry letters · 2024Article
- Fast Quantitative Validation of 3D Models of Low-Affinity Protein-Ligand Complexes by STD NMR Spectroscopy.Journal of medicinal chemistry · 2024Article
- Modulation of Multidrug Resistance Protein 1-mediated Transport Processes by the Antiviral Drug Ritonavir in Cultured Primary Astrocytes.Neurochemical research · 2024Article
- Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex.Journal of chemical theory and computation · 2023Article
- Identifying and overcoming the sampling challenges in relative binding free energy calculations of a model protein:protein complex.bioRxiv : the preprint server for biology · 2023Article
- Open Binding Pose Metadynamics: An Effective Approach for the Ranking of Protein-Ligand Binding Poses.Journal of chemical information and modeling · 2022Article
- Combined Free-Energy Calculation and Machine Learning Methods for Understanding Ligand Unbinding Kinetics.Journal of chemical theory and computation · 2022Article
- New perspectives in cancer drug development: computational advances with an eye to design.RSC medicinal chemistry · 2021Review
- Machine Learning and Enhanced Sampling Simulations for Computing the Potential of Mean Force and Standard Binding Free Energy.Journal of chemical theory and computation · 2021Article
- From the Design to theJournal of medicinal chemistry · 2021Article
- The role of water in host-guest interaction.Nature communications · 2021Article
Corrections and comments
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Authors and funding
6 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Calculating absolute binding free energies is challenging and important. In this paper, we test some recently developed metadynamics-based methods and develop a new combination with a Hamiltonian replica-exchange approach. The methods were tested on 18 chemically diverse ligands with a wide range of different binding affinities to a complex target; namely, human soluble epoxide hydrolase. The results suggest that metadynamics with a funnel-shaped restraint can be used to calculate, in a computationally affordable and relatively accurate way, the absolute binding free energy for small fragments. When used in combination with an optimal pathlike variable obtained using machine learning or with the Hamiltonian replica-exchange algorithm SWISH, this method can achieve reasonably accurate results for increasingly complex ligands, with a good balance of computational cost and speed. An additional benefit of using the combination of metadynamics and SWISH is that it also provides useful information about the role of water in the binding mechanism.
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