ArticleJournal of computer-aided molecular design2019
Evaluating the performance of MM/PBSA for binding affinity prediction using class A GPCR crystal structures.
Article in Journal of computer-aided molecular design, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Mapping partial agonism of mitragynine at the µ-opioid receptor through molecular dynamics and Markov state modelling analysis.Scientific reports · 2026Article
- Integrated Computer-Aided Drug Design: Advances in GPCR Natural Ligand Discovery.Cell biochemistry and biophysics · 2026Review
- Theoretical study of KRAS G12C secondary mutations influencing inhibitor resistance.Biophysics and physicobiology · 2026Article
- Computational Pipeline for Accelerating the Design of Glycomimetics.Journal of chemical information and modeling · 2025Article
- Computation of Protein-Ligand Binding Free Energies with a Quantum Mechanics-Based Mining Minima Algorithm.Journal of chemical theory and computation · 2025Article
- Molecular Dynamics Simulation Studies of Beta-Glucogallin and Dihydro Dehydro Coniferyl Alcohol from Syzygium cumini for its Antimicrobial Activity on Staphylococcus aureus.Cell biochemistry and biophysics · 2025Article
- A head-to-head comparison of MM/PBSA and MM/GBSA in predicting binding affinities for the CBJournal of molecular modeling · 2024Article
- Consensus scoring evaluated using the GPCR-Bench dataset: Reconsidering the role of MM/GBSA.Journal of computer-aided molecular design · 2022Article
- Generalized Methodology for the Quick Prediction of Variant SARS-CoV-2 Spike Protein Binding Affinities with Human Angiotensin-Converting Enzyme II.The journal of physical chemistry. B · 2022Article
- Fast Prediction of Binding Affinities of the SARS-CoV-2 Spike Protein Mutant N501Y (UK Variant) with ACE2 and Miniprotein Drug Candidates.The journal of physical chemistry. B · 2021Article
- G protein-coupled receptors: structure- and function-based drug discovery.Signal transduction and targeted therapy · 2021Review
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- Benchmarking the performance of MM/PBSA in virtual screening enrichment using the GPCR-Bench dataset.Journal of computer-aided molecular design · 2020Article
- Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor HJournal of computer-aided molecular design · 2020Article
- Auraptene inhibits migration, invasion and metastatic behavior of human malignant glioblastoma cells: AnAvicenna journal of phytomedicineArticle
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5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The recent expansion of GPCR crystal structures provides the opportunity to assess the performance of structure-based drug design methods for the GPCR superfamily. Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA)-based methods are commonly used for binding affinity prediction, as they provide an intermediate compromise of speed and accuracy between the empirical scoring functions used in docking and more robust free energy perturbation methods. In this study, we systematically assessed the performance of MM/PBSA in predicting experimental binding free energies using twenty Class A GPCR crystal structures and 934 known ligands. Correlations between predicted and experimental binding free energies varied significantly between individual targets, ranging from r = - 0.334 in the inactive-state CB
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