ReviewAnnual review of biophysics2019
Generalized Born Implicit Solvent Models for Biomolecules.
Review in Annual review of biophysics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 138 papers.
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Who cites it
138 citing papers in PubMed.
- Bluues2: An enhanced web server for fast and accurate electrostatic analysis of proteins and protein complexes.Protein science : a publication of the Protein Society · 2026Article
- Think Beyond The Core: Computationally Decoding the Hydrophilic Corona of Drug-Loaded Polymer Micelles.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Discovery of two novel small-molecule series with potent SARS-CoV-2 inhibitionChemical science · 2026Article
- Dissecting Structural and Functional Determinants of Microtubules Stabilization through Guided Chemical Modulation.Journal of medicinal chemistry · 2026Article
- Mapping Trofinetide Polypharmacology in Rett Syndrome: A Multi-Stage Computational Analysis.Journal of computational chemistry · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.Journal of chemical theory and computation · 2026Article
- Quantifying Small-Molecule Association with Lipid Membranes: Methods, Models, and Limitations.Membranes · 2026Review
- Pathway Representation via Intrinsic Structural Medoids (PRISM): A Structural Mapping Approach to Clustering Molecular Pathways.bioRxiv : the preprint server for biology · 2026Article
- Computational discovery and repurposing of chloramphenicol succinate as a potent P2YJournal of advanced research · 2026Article
- Ensemble Sensitivity to Chemical Modifications in Free and Bound Macrocyclic Peptides.The journal of physical chemistry. B · 2026Article
- AmberTorchPB: A Unified Framework for Poisson-Boltzmann-Based Reaction Field Energy Calculation via Tensor Computation.Journal of chemical theory and computation · 2026Article
- The impact of PD-1 mutations on pembrolizumab binding: insights from molecular dynamics and MM-GBSA analysis.Scientific reports · 2026Article
- Knowledge Distillation of a Protein Language Model Yields a Foundational Implicit Solvent Model.ArXiv · 2026Article
- Network analysis-guided drug repurposing: IGF1R as a novel melanoma target and therapeutic potential of dapagliflozin.Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences · 2026Article
- A Computational Structural Analysis of Host Insertions in the Polyproline Region of the Hepatitis E Virus pORF1 Polyprotein.Viruses · 2026Article
- A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein-Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases.Journal of chemical information and modeling · 2026Article
- Phosphorylation of a Tumor-Derived ASXL2 Epitope Remodels the HLA-Bound Peptide Conformational Ensemble and Interaction Network of the Peptide-HLA Complex.Computational and structural biotechnology journal · 2026Article
- Designing novel linagliptin analogs through combined generative artificial intelligence, molecular docking, molecular dynamics simulation, and binding energy estimation for targeting fibroblast activation protein.Frontiers in chemistry · 2026Article
- Computational and experimental analysis of oleanolic acid as an allosteric activator of SIRT1.Turkish journal of chemistry · 2026Article
- Mechanistic basis for the opposing effects of H2A and H2B ubiquitination on nucleosome stability and dynamics.Epigenetics & chromatin · 2025Article
78 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
It would often be useful in computer simulations to use an implicit description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation and can be very efficient compared to the explicit treatment of the solvent. Here, we review a particular class of so-called fast implicit solvent models, generalized Born (GB) models, which are widely used for molecular dynamics (MD) simulations of proteins and nucleic acids. These approaches model hydration effects and provide solvent-dependent forces with efficiencies comparable to molecular-mechanics calculations on the solute alone; as such, they can be incorporated into MD or other conformational searching strategies in a straightforward manner. The foundations of the GB model are reviewed, followed by examples of newer, emerging models and examples of important applications. We discuss their strengths and weaknesses, both for fidelity to the underlying continuum model and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations.
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