ArticleFrontiers in molecular biosciences2019
Accurate Biomolecular Simulations Account for Electronic Polarization.
Article in Frontiers in molecular biosciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
- Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors.Communications biology · 2025Article
- An Adaptive Force Matching Potential for Alanine Developed with Møller-Plesset Perturbation Theory and Smooth Fourier Transform Correction Map.The journal of physical chemistry. B · 2025Article
- The Q-AMOEBA (CF) Polarizable Potential.The journal of physical chemistry letters · 2025Article
- High-Resolution Molecular-Dynamics Simulations of the Pyruvate Kinase Muscle Isoform 1 and 2 (PKM1/2).Chemistry (Weinheim an der Bergstrasse, Germany) · 2025Article
- Histidine 73 methylation coordinates β-actin plasticity in response to key environmental factors.Nature communications · 2025Article
- Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field.Journal of chemical theory and computation · 2024Article
- Force-field-enhanced neural network interactions: from local equivariant embedding to atom-in-molecule properties and long-range effects.Chemical science · 2023Article
- Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-polarizable Force Fields.Journal of chemical theory and computation · 2023Article
- Nonaqueous Ion Pairing Exemplifies the Case for Including Electronic Polarization in Molecular Dynamics Simulations.The journal of physical chemistry letters · 2023Article
- Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects.Chemical science · 2023Article
- Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set.Journal of chemical theory and computation · 2022Article
- Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations.Journal of chemical theory and computation · 2022Article
- Computationally driven discovery of SARS-CoV-2 MChemical science · 2022Article
- Atomic Polarizabilities for Interactive Dipole Induction Models.Journal of chemical information and modeling · 2022Article
- Article
- The mutual interactions of RNA, counterions and water - quantifying the electrostatics at the phosphate-water interface.Chemical communications (Cambridge, England) · 2021Review
- Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV-2 Main Protease Dimerization Interface.The journal of physical chemistry letters · 2021Article
- Atomistic Polarizable Embeddings: Energy, Dynamics, Spectroscopy, and Reactivity.Accounts of chemical research · 2021Article
- Charge State Dependence of Amino Acid Propensity at Water Surface: Mechanisms Elucidated by Molecular Dynamics Simulations.The journal of physical chemistry. A · 2021Article
- Biomolecular Modeling and Simulation: A Prospering Multidisciplinary Field.Annual review of biophysics · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this perspective, we discuss where and how accounting for electronic many-body polarization affects the accuracy of classical molecular dynamics simulations of biomolecules. While the effects of electronic polarization are highly pronounced for molecules with an opposite total charge, they are also non-negligible for interactions with overall neutral molecules. For instance, neglecting these effects in important biomolecules like amino acids and phospholipids affects the structure of proteins and membranes having a large impact on interpreting experimental data as well as building coarse grained models. With the combined advances in theory, algorithms and computational power it is currently realistic to perform simulations with explicit polarizable dipoles on systems with relevant sizes and complexity. Alternatively, the effects of electronic polarization can also be included at zero additional computational cost compared to standard fixed-charge force fields using the electronic continuum correction, as was recently demonstrated for several classes of biomolecules.
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