ArticleJournal of chemical theory and computation2018
Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
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- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- A head-to-head comparison of MM/PBSA and MM/GBSA in predicting binding affinities for the CBJournal of molecular modeling · 2024Article
- Inclusion of Water Multipoles into the Implicit Solvation Framework Leads to Accuracy Gains.The journal of physical chemistry. B · 2024Article
- PEP-Patch: Electrostatics in Protein-Protein Recognition, Specificity, and Antibody Developability.Journal of chemical information and modeling · 2023Article
- Uncovering water effects in protein-ligand recognition: importance in the second hydration shell and binding kinetics.Physical chemistry chemical physics : PCCP · 2023Article
- A Closed-Form, Analytical Approximation for Apparent Surface Charge and Electric Field of Molecules.ACS omega · 2022Article
- A Physics-Guided Neural Network for Predicting Protein-Ligand Binding Free Energy: From Host-Guest Systems to the PDBbind Database.Biomolecules · 2022Article
- Systematic analysis and molecular profiling of EGFR allosteric inhibitor cross-reactivity across the proto-oncogenic ErbB family kinases by integrating dynamics simulation, energetics calculation and biochemical assay.European biophysics journal : EBJ · 2022Article
- Computational Tools for Accurate Binding Free-Energy Prediction.Methods in molecular biology (Clifton, N.J.) · 2022Article
- An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor.Molecules (Basel, Switzerland) · 2021Article
- MMGB/SA Consensus Estimate of the Binding Free Energy Between the Novel Coronavirus Spike Protein to the Human ACE2 Receptor.bioRxiv : the preprint server for biology · 2020Article
- Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.Journal of chemical theory and computation · 2020Article
- ROBUSTNESS OF MULTIDIMENSIONAL OPTIMIZATION OUTCOMES: A GENERAL APPROACH AND A CASE STUDY.Spring simulation conference (SpringSim) · 2020Article
- Generalized Born Implicit Solvent Models for Biomolecules.Annual review of biophysics · 2019Review
- Explicit ions/implicit water generalized Born model for nucleic acids.The Journal of chemical physics · 2018Article
- Theoretical Study of the β-Cyclodextrin Inclusion Complex Formation of Eugenol in Water.Molecules (Basel, Switzerland) · 2018Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
The need for accurate yet efficient representation of the aqueous environment in biomolecular modeling has led to the development of a variety of generalized Born (GB) implicit solvent models. While many studies have focused on the accuracy of available GB models in predicting solvation free energies, a systematic assessment of the quality of these models in binding free energy calculations, crucial for rational drug design, has not been undertaken. Here, we evaluate the accuracies of eight common GB flavors (GB-HCT, GB-OBC, GB-neck2, GBNSR6, GBSW, GBMV1, GBMV2, and GBMV3), available in major molecular dynamics packages, in predicting the electrostatic binding free energies ( ΔΔ G
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