ArticleJournal of chemical theory and computation2015
Physics-Based Potentials for Coarse-Grained Modeling of Protein-DNA Interactions.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 23 citations in OpenAlex.
- Determination of Nucleotide-Nucleotide and Nucleotide-Amino Acid Binding Interactions from All-Atom Potential-of-Mean-Force Calculations.ACS physical chemistry Au · 2026Article
- Coarse-grained RNA model for the Martini 3 force field.Biophysical journal · 2026Article
- Early Stages of RNA-Mediated Conversion of Human Prions.The journal of physical chemistry. B · 2022Article
- Coarse-grained modeling of the calcium, sodium, magnesium and potassium cations interacting with proteins.Journal of molecular modeling · 2022Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- Bottom-Up Coarse-Grained Modeling of DNA.Frontiers in molecular biosciences · 2021Review
- Finite Element Analysis for Predicting Skin Pharmacokinetics of Nano Transdermal Drug Delivery System Based on the Multilayer Geometry Model.International journal of nanomedicine · 2020Article
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.Journal of computational chemistry · 2018Article
- Martini Coarse-Grained Force Field: Extension to RNA.Biophysical journal · 2017Article
- The "sugar" coarse-grained DNA model.Journal of molecular modeling · 2017Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
Abstract
Physics-based potentials have been developed for the interactions between proteins and DNA for simulations with the UNRES + NARES-2P force field. The mean-field interactions between a protein and a DNA molecule can be divided into eight categories: (1) nonpolar side chain–DNA base, (2) polar uncharged side chain–DNA base, (3) charged side chain–DNA base, (4) peptide group–phosphate group, (5) peptide group–DNA base, (6) nonpolar side chain–phosphate group, (7) polar uncharged side chain–phosphate group, and (8) charged side chain–phosphate group. Umbrella-sampling molecular dynamics simulations in explicit TIP3P water using the AMBER force field were carried out to determine the potentials of mean force (PMF) for all 105 pairs of interacting components. Approximate analytical expressions for the mean-field interaction energy of each pair of the different kinds of interacting molecules were then fitted to the PMFs to obtain the parameters of the analytical expressions. These analytical expressions can reproduce satisfactorily the PMF curves corresponding to different orientations of the interacting molecules. The results suggest that the physics-based mean-field potentials of amino acid–nucleotide interactions presented here can be used in coarse-grained simulation of protein–DNA interactions.
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