ArticleJournal of computer-aided molecular design2018
Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking.
Article in Journal of computer-aided molecular design, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Farnesoid X receptor (FXR) as a potential therapeutic target for lung diseases: a narrative review.Journal of thoracic disease · 2024Review
- The effect of protein mutations on drug binding suggests ensuing personalised drug selection.Scientific reports · 2021Article
- Estimating the Roles of Protonation and Electronic Polarization in Absolute Binding Affinity Simulations.Journal of chemical theory and computation · 2021Article
- Accounting for the Central Role of Interfacial Water in Protein-Ligand Binding Free Energy Calculations.Journal of chemical theory and computation · 2020Article
- Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens.International journal of molecular sciences · 2020Review
- D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.Journal of computer-aided molecular design · 2020Article
- Role of Farnesoid X Receptor in the Pathogenesis of Respiratory Diseases.Canadian respiratory journal · 2020Review
- Uncertainty Quantification in Alchemical Free Energy Methods.Journal of chemical theory and computation · 2018Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have studied the binding of 102 ligands to the farnesoid X receptor within the D3R Grand Challenge 2016 blind-prediction competition. First, we employed docking with five different docking software and scoring functions. The selected docked poses gave an average root-mean-squared deviation of 4.2 Å. Consensus scoring gave decent results with a Kendall's τ of 0.26 ± 0.06 and a Spearman's ρ of 0.41 ± 0.08. For a subset of 33 ligands, we calculated relative binding free energies with free-energy perturbation. Five transformations between the ligands involved a change of the net charge and we implemented and benchmarked a semi-analytic correction (Rocklin et al., J Chem Phys 139:184103, 2013) for artifacts caused by the periodic boundary conditions and Ewald summation. The results gave a mean absolute deviation of 7.5 kJ/mol compared to the experimental estimates and a correlation coefficient of R
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