ArticleJournal of computational chemistry2018
A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.
Article in Journal of computational chemistry, 2018. 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, 17 citations in OpenAlex.
- Modeling the Homologous Recombination Process: Methods, Successes and Challenges.International journal of molecular sciences · 2023Review
- Early Stages of RNA-Mediated Conversion of Human Prions.The journal of physical chemistry. B · 2022Article
- Computationally exploring the mechanism of bacteriophage T7 gp4 helicase translocating along ssDNA.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- Residue-Level Contact Reveals Modular Domain Interactions of PICK1 Are Driven by Both Electrostatic and Hydrophobic Forces.Frontiers in molecular biosciences · 2020Article
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Based on the coarse-grained UNRES and NARES-2P models of proteins and nucleic acids, respectively, developed in our laboratory, in this work we have developed a coarse-grained model of systems containing proteins and nucleic acids. The UNRES and NARES-2P effective energy functions have been applied to the protein and nucleic-acid components of a system, respectively, while protein-nucleic-acid interactions have been described by the respective coarse-grained potentials developed in our recent work (Yin et al., J. Chem Theory Comput. 2015, 11, 1792). The Debye-Hückel screening has been applied to the electrostatic-interaction energy between the phosphate groups and charged amino-acid side chains. The model has been integrated into the UNRES package for coarse-grained molecular dynamics simulations of proteins and the implementation has been tested for energy conservation in microcanonical molecular dynamics runs and for temperature conservation in canonical molecular dynamics runs. Two case studies were performed: (i) the dynamics of the Ku protein heterodimer bound to DNA, for which it was found that the Ku70/Ku80 protein complex plays an active role in DNA repairing and (ii) conformational changes of the multiple antibiotic resistance (MarA) protein occurring during DNA binding, for which the functionally important motions occurring during this process were identified. © 2018 Wiley Periodicals, Inc.
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