ArticleEuropean biophysics journal : EBJ2022
Molecular dynamics simulation or structure refinement of proteins: are solvent molecules required? A case study using hen lysozyme.
Article in European biophysics journal : EBJ, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 13 citations in OpenAlex.
- Fluctuating β-Sheet Secondary Structure in DS119 Explains the Small Effects of Backbone N-Amination on Thermal Stability.Journal of peptide science : an official publication of the European Peptide Society · 2026Article
- Dual targeting of IGF-1R and K-RAS with natural phytochemicals for lung cancer therapy: an in-silico study.Journal, genetic engineering & biotechnology · 2026Article
- Synthesis, characterization and bio-evaluation of novel series of pyrazoline derivatives as potential antifungal agents.Scientific reports · 2025Article
- Design, synthesis, and inhibitory activity of hydroquinone ester derivatives against mushroom tyrosinase.RSC advances · 2024Article
- Solvent Accessibility Promotes Rotamer Errors during Protein Modeling with Major Side-Chain Prediction Programs.Journal of chemical information and modeling · 2023Article
- Repurposing Anti-Dengue Compounds against Monkeypox Virus Targeting Core Cysteine Protease.Biomedicines · 2023Article
- Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference.Biophysical reviews · 2022Review
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Authors and funding
4 authors at 4 institutions in 3 countries.
Funding
Abstract
In protein simulation or structure refinement based on values of observable quantities measured in (aqueous) solution, solvent (water) molecules may be explicitly treated, omitted, or represented by a potential of mean-solvation-force term, depending on protein coordinates only, in the force field used. These three approaches are compared for hen egg white lysozyme (HEWL). This 129-residue non-spherical protein contains a variety of secondary-structure elements, and ample experimental data are available: 1630 atom-atom Nuclear Overhauser Enhancement (NOE) upper distance bounds, 213
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