ReviewEuropean journal of medicinal chemistry2015
Implicit solvent methods for free energy estimation.
Review in European journal of medicinal chemistry, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Predicting Solvation Free Energies of Molecules and Ions via First-Principles and Machine-Learning Molecular Dynamics.Journal of chemical theory and computation · 2026Article
- Structural Modulation of TpPa‑1 Covalent Organic Framework in Flow Synthesis Guided by Green Chemistry Principles.ACS engineering Au · 2026Article
- Floridoside as a Hinge-Targeted Inhibitor of MAPK13: Atomistic Insights from Molecular Dynamics Simulations.Marine drugs · 2026Article
- A diverse and chemically relevant solvation model benchmark set with flexible molecules and conformer ensembles.Chemical science · 2025Article
- Implicit Solvent Models and Their Applications in Biophysics.Biomolecules · 2025Review
- Excited-state nonadiabatic dynamics in explicit solvent using machine learned interatomic potentials.Digital discovery · 2025Article
- On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super-Gaussian Poisson-Boltzmann model.Journal of computational chemistry · 2025Article
- Calculation of protein-ligand binding entropies using a rule-based molecular fingerprint.Biophysical journal · 2024Article
- An Update in Computational Methods for Environmental Monitoring: Theoretical Evaluation of the Molecular and Electronic Structures of Natural Pigment-Metal Complexes.Molecules (Basel, Switzerland) · 2024Review
- Molecular Dynamics as a Tool for Virtual Ligand Screening.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Arbitrary-Shape Dielectric Particles Interacting in the Linearized Poisson-Boltzmann Framework: An Analytical Treatment.The journal of physical chemistry. B · 2022Article
- Recent Developments in Methicillin-ResistantAntibiotics (Basel, Switzerland) · 2022Review
- Computational modeling of protein conformational changes - Application to the opening SARS-CoV-2 spike.Journal of computational physics · 2021Article
- Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field.Journal of chemical theory and computation · 2021Article
- Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.Chemical reviews · 2020Review
- Data-Driven Molecular Dynamics: A Multifaceted Challenge.Pharmaceuticals (Basel, Switzerland) · 2020Review
- Targeting the Protein Tunnels of the Urease Accessory Complex: A Theoretical Investigation.Molecules (Basel, Switzerland) · 2020Article
- Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model.Journal of computational chemistry · 2018Article
- Dynamic Docking: A Paradigm Shift in Computational Drug Discovery.Molecules (Basel, Switzerland) · 2017Review
- "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.Journal of computational chemistry · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Solvation is a fundamental contribution in many biological processes and especially in molecular binding. Its estimation can be performed by means of several computational approaches. The aim of this review is to give an overview of existing theories and methods to estimate solvent effects giving a specific focus on the category of implicit solvent models and their use in Molecular Dynamics. In many of these models, the solvent is considered as a continuum homogenous medium, while the solute can be represented at the atomic detail and at different levels of theory. Despite their degree of approximation, implicit methods are still widely employed due to their trade-off between accuracy and efficiency. Their derivation is rooted in the statistical mechanics and integral equations disciplines, some of the related details being provided here. Finally, methods that combine implicit solvent models and molecular dynamics simulation, are briefly described.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.