ArticleJournal of computational chemistry2010
Coarse-grained model of nucleic acid bases.
Article in Journal of computational chemistry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- The "sugar" coarse-grained DNA model.Journal of molecular modeling · 2017Article
- My 65 years in protein chemistry.Quarterly reviews of biophysics · 2015Review
- DNA Duplex Formation with a Coarse-Grained Model.Journal of chemical theory and computation · 2014Article
- Close encounters with DNA.Journal of physics. Condensed matter : an Institute of Physics journal · 2014Review
- A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment.Journal of chemical theory and computation · 2014Article
- A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.Journal of molecular modeling · 2014Article
- An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization.The Journal of chemical physics · 2013Article
- Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix.Physical review letters · 2013Article
- Moving beyond Watson-Crick models of coarse grained DNA dynamics.The Journal of chemical physics · 2011Article
- Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models.Journal of computer-aided molecular design · 2011Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Atomistic simulations of nucleic acids are prohibitively expensive and, consequently, reduced models of these compounds are of great interest in the field. In this work, we propose a physics-based coarse-grained model of nucleic-acid bases in which each base is represented by several (3-5) interaction centers. van der Waals interactions are modeled by Lennard-Jones spheres with a 12-6 potential energy function. The charge distribution is modeled by a set of electric dipole moments located at the centers of the Lennard-Jones spheres. The method for computing the Lennard-Jones parameters, electric dipole moments (their magnitude and orientation) and positions of the interaction centers is described. Several models with different numbers of interaction centers were tested. The model with three-center cytosine, four-center guanine, four-center thymine, and five-center adenine satisfactorily reproduces the canonical Watson-Crick hydrogen bonding and stacking interaction energies of the all-atom AMBER model. The computation time with the coarse-grained model is reduced seven times compared with that of the all-atom model.
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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.