ArticleChemical science2023
The role of loop dynamics in the prediction of ligand-protein binding enthalpy.
Article in Chemical science, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- MSCA-PLA: multi-scale cross-attention with differentiable pooling for protein-ligand binding affinity prediction.Molecular diversity · 2026Article
- Structural characterization of representative odorant receptors in Rhynchophorus ferrugineus through high-throughput modelling and extended molecular dynamics simulations.Journal of computer-aided molecular design · 2026Article
- Water Networks as Hydrophobic Recognition Motifs in Proteins.Angewandte Chemie (International ed. in English) · 2026Article
- Chemoinformatic Approaches to Identify Bioactive Inhibitors Against Type I Dehydroquinase (DHQ1) Enzyme of TyphoidalBioinformatics and biology insights · 2026Article
- Partially Sulfated Pillar[5]Arenes: Synthesis and Molecular Recognition Properties.Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Motif-VI loop acts as a nucleotide valve in the West Nile Virus NS3 Helicase.Nucleic acids research · 2024Article
- Computed Protein-Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems.Journal of chemical information and modeling · 2023Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The enthalpic and entropic components of ligand-protein binding free energy reflect the interactions and dynamics between ligand and protein. Despite decades of study, our understanding and hence our ability to predict these individual components remains poor. In recent years, there has been substantial effort and success in the prediction of relative and absolute binding free energies, but the prediction of the enthalpic (and entropic) contributions in biomolecular systems remains challenging. Indeed, it is not even clear what kind of performance in terms of accuracy could currently be obtained for such systems. It is, however, relatively straight-forward to compute the enthalpy of binding. We thus evaluated the performance of absolute enthalpy of binding calculations using molecular dynamics simulation for ten inhibitors against a member of the bromodomain family, BRD4-1, against isothermal titration calorimetry data. Initial calculations, with the AMBER force-field showed good agreement with experiment (
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