ArticleBiophysical journal2003
DNA polymorphism: a comparison of force fields for nucleic acids.
Article in Biophysical journal, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Benchmark assessment of molecular geometries and energies from small molecule force fields.F1000Research · 2020Article
- Mechanical evolution of DNA double-strand breaks in the nucleosome.PLoS computational biology · 2018Article
- Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation.Nucleic acids research · 2015Article
- Article
- The ABCs of molecular dynamics simulations on B-DNA, circa 2012.Journal of biosciences · 2012Review
- Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.Journal of chemical theory and computation · 2012Article
- Evaluation of DNA Force Fields in Implicit Solvation.Journal of chemical theory and computation · 2011Article
- Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles.Journal of chemical theory and computation · 2011Article
- Molecular dynamics study of solvation effect on diffusivity changes of DNA fragments.Journal of molecular modeling · 2011Article
- Extensive protein and DNA backbone sampling improves structure-based specificity prediction for C2H2 zinc fingers.Nucleic acids research · 2011Article
- Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model.The journal of physical chemistry. B · 2011Article
- In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form.Nucleic acids research · 2009Article
- CHARMM: the biomolecular simulation program.Journal of computational chemistry · 2009Review
- Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy.Nano letters · 2008Article
- Dissociation of minor groove binders from DNA: insights from metadynamics simulations.Nucleic acids research · 2008Article
- Important genetic checkpoints for insulin resistance in salt-sensitive (S) Dahl rats.Cardiovascular diabetology · 2008Article
- Sliding of alkylating anticancer drugs along the minor groove of DNA: new insights on sequence selectivity.Biophysical journal · 2008Article
- Vibrational stark effect probes for nucleic acids.The journal of physical chemistry. B · 2007Article
- The B- to A-DNA transition and the reorganization of solvent at the DNA surface.Biophysical journal · 2005Article
- Structure and energy of a DNA dodecamer under tensile load.Nucleic acids research · 2005Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the latter two is the primary focus of this paper. The performance of each force field is evaluated first on its ability to reproduce the B-DNA decamer d(CGATTAATCG)(2) in solution with simulations in which the long-range electrostatics were treated by the particle mesh Ewald method; the crystal structure determined by Quintana et al. (1992) is used as the starting point for all simulations. A detailed analysis of the structural and solvation properties shows how well the different force fields can reproduce sequence-specific features. The results are compared with data from experimental and previous theoretical studies.
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