Next Article in Journal
Cannabidiol in Skin Health: A Comprehensive Review of Topical Applications in Dermatology and Cosmetic Science
Previous Article in Journal
Isolation and Identification of Duck Intestinal Probiotics and Their Effects on the Production and Immune Performance of Pekin Ducks
 
 
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Review

Implicit Solvent Models and Their Applications in Biophysics

by
Yusuf Bugra Severoglu
1,
Betul Yuksel
1,
Cagatay Sucu
1,
Nese Aral
1,
Vladimir N. Uversky
2,* and
Orkid Coskuner-Weber
1,*
1
Molecular Biotechnology, Turkish-German University, Sahinkaya Caddesi No. 106, Beykoz, 34820 Istanbul, Turkey
2
Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
*
Authors to whom correspondence should be addressed.
Biomolecules 2025, 15(9), 1218; https://doi.org/10.3390/biom15091218 (registering DOI)
Submission received: 30 July 2025 / Revised: 16 August 2025 / Accepted: 20 August 2025 / Published: 23 August 2025
(This article belongs to the Special Issue Protein Biophysics)

Abstract

:Solvents represent the quiet majority in biomolecular systems, yet modeling their influence with both speed and ri:gor remains a central challenge. This study maps the state of the art in implicit solvent theory and practice, spanning classical continuum electrostatics (PB/GB; DelPhi, APBS), modern nonpolar and cavity/dispersion treatments, and quantum–continuum models (PCM, COSMO/COSMO-RS, SMx/SMD). We highlight where these methods excel and where they falter, namely, around ion specificity, heterogeneous interfaces, entropic effects, and parameter sensitivity. We then spotlight two fast-moving frontiers that raise both accuracy and throughput: machine learning-augmented approaches that serve as PB-accurate surrogates, learn solvent-averaged potentials for MD, or supply residual corrections to GB/PB baselines, and quantum-centric workflows that couple continuum solvation methods, such as IEF-PCM, to sampling on real quantum hardware, pointing toward realistic solution-phase electronic structures at emerging scales. Applications across protein–ligand binding, nucleic acids, and intrinsically disordered proteins illustrate how implicit models enable rapid hypothesis testing, large design sweeps, and long-time sampling. Our perspective argues for hybridization as a best practice, meaning continuum cores refined by improved physics, such as multipolar water, ML correctors with uncertainty quantification and active learning, and quantum–continuum modules for chemically demanding steps.
Keywords: implicit solvent models; biomolecular simulations; Poisson–Boltzmann equation; Generalized Born model; protein–ligand binding implicit solvent models; biomolecular simulations; Poisson–Boltzmann equation; Generalized Born model; protein–ligand binding

Share and Cite

MDPI and ACS Style

Severoglu, Y.B.; Yuksel, B.; Sucu, C.; Aral, N.; Uversky, V.N.; Coskuner-Weber, O. Implicit Solvent Models and Their Applications in Biophysics. Biomolecules 2025, 15, 1218. https://doi.org/10.3390/biom15091218

AMA Style

Severoglu YB, Yuksel B, Sucu C, Aral N, Uversky VN, Coskuner-Weber O. Implicit Solvent Models and Their Applications in Biophysics. Biomolecules. 2025; 15(9):1218. https://doi.org/10.3390/biom15091218

Chicago/Turabian Style

Severoglu, Yusuf Bugra, Betul Yuksel, Cagatay Sucu, Nese Aral, Vladimir N. Uversky, and Orkid Coskuner-Weber. 2025. "Implicit Solvent Models and Their Applications in Biophysics" Biomolecules 15, no. 9: 1218. https://doi.org/10.3390/biom15091218

APA Style

Severoglu, Y. B., Yuksel, B., Sucu, C., Aral, N., Uversky, V. N., & Coskuner-Weber, O. (2025). Implicit Solvent Models and Their Applications in Biophysics. Biomolecules, 15(9), 1218. https://doi.org/10.3390/biom15091218

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Article metric data becomes available approximately 24 hours after publication online.
Back to TopTop