A nucleotide-level coarse-grained model of RNA

A nucleotide-level coarse-grained model of RNA

We present a new, nucleotide-level model for RNA, oxRNA, based on the coarse-graining methodology recently developed for the oxDNA model of DNA. The model is designed to reproduce structural, mechanical, and thermodynamic properties of RNA, and the coarse-graining level aims to retain the relevant p...

Disgrifiad llawn

Manylion Llyfryddiaeth
Prif Awduron:	Šulc, P, Romano, F, Ouldridge, T, Doye, J, Louis, A
Fformat:	Journal article
Iaith:	English
Cyhoeddwyd:	American Institute of Physics 2014

Eitemau Tebyg

Coarse-grained modeling of DNA and DNA nanotechnology
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2012)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
gan: Šulc, P, et al.
Cyhoeddwyd: (2014)

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model
gan: Sulc, P, et al.
Cyhoeddwyd: (2012)

Sequence-dependent thermodynamics of a coarse-grained DNA model.
gan: Šulc, P, et al.
Cyhoeddwyd: (2012)

Coarse-grained modelling of supercoiled RNA
gan: Matek, C, et al.
Cyhoeddwyd: (2015)

Coarse-grained simulations of DNA overstretching.
gan: Romano, F, et al.
Cyhoeddwyd: (2013)

Coarse-grained modelling of DNA-RNA hybrids
gan: Ratajczyk, EJ, et al.
Cyhoeddwyd: (2023)

DNA nanotweezers studied with a coarse-grained model of DNA.
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2010)

DNA nanotweezers studied with a coarse-grained model of DNA
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2010)

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model.
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2011)

Coarse-graining DNA for simulations of DNA nanotechnology.
gan: Doye, J, et al.
Cyhoeddwyd: (2013)

Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model
gan: Harrison, R, et al.
Cyhoeddwyd: (2019)

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.
gan: Snodin, B, et al.
Cyhoeddwyd: (2015)

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly
gan: Fonseca, P, et al.
Cyhoeddwyd: (2018)

Modelling toehold-mediated RNA strand displacement
gan: Šulc, P, et al.
Cyhoeddwyd: (2015)

Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker.
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2013)

Free energy landscapes of DNA and its assemblies: perspectives from coarse-grained modelling
gan: Doye, JPK, et al.
Cyhoeddwyd: (2022)

Coarse-grained modelling of the structural properties of DNA origami
gan: Snodin, B, et al.
Cyhoeddwyd: (2019)

Coarse-grained modelling of nucleic acids
gan: Sulc, P
Cyhoeddwyd: (2014)

Coarse-Grained Modelling of Extreme DNA Bending
gan: Harrison, R, et al.
Cyhoeddwyd: (2014)

Coarse-grained modelling of DNA and DNA self-assembly
gan: Ouldridge, T
Cyhoeddwyd: (2011)

Characterizing the motion of jointed DNA nanostructures using a coarse-grained model
gan: Sharma, R, et al.
Cyhoeddwyd: (2017)

Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.
gan: Schreck, J, et al.
Cyhoeddwyd: (2016)

DNA hybridization kinetics: zippering, internal displacement and sequence dependence.
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2013)

DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
gan: Schreck, J, et al.
Cyhoeddwyd: (2014)

Characterizing the bending and flexibility induced by bulges in DNA duplexes.
gan: Schreck, J, et al.
Cyhoeddwyd: (2015)

Coarse-graining polymers as soft colloids
gan: Louis, A, et al.
Cyhoeddwyd: (2002)

The effect of topology on the structure and free energy landscape of DNA kissing complexes.
gan: Romano, F, et al.
Cyhoeddwyd: (2012)

The role of loop stacking in the dynamics of DNA hairpin formation.
gan: Mosayebi, M, et al.
Cyhoeddwyd: (2014)

The self-assembly of DNA Holliday junctions studied with a minimal model
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2009)

Extracting bulk properties of self-assembling systems from small simulations.
gan: Ouldridge, T, et al.
Cyhoeddwyd: (2010)

Plectoneme tip bubbles : coupled denaturation and writhing in supercoiled DNA
gan: Matek, C, et al.
Cyhoeddwyd: (2015)

Representability problems for coarse-grained water potentials.
gan: Johnson, M, et al.
Cyhoeddwyd: (2007)

On the biophysics and kinetics of toehold-mediated DNA strand displacement
gan: Srinivas, N, et al.
Cyhoeddwyd: (2013)

Towards coarse-grained modelling of proteins
gan: M.Stepanova
Cyhoeddwyd: (2007-09-01)

Coarse-Graining of Observables
gan: Stan Gudder
Cyhoeddwyd: (2022-10-01)

Many-body interactions and correlations in coarse-grained descriptions of polymer solutions.
gan: Bolhuis, P, et al.
Cyhoeddwyd: (2001)

Many-body interactions and correlations in coarse-grained descriptions of polymer solutions.
gan: Bolhuis, P, et al.
Cyhoeddwyd: (2001)

Bottom-up coarse-grained modeling of DNA
gan: Sun, Tiedong, et al.
Cyhoeddwyd: (2021)

Coarse-graining diblock copolymer solutions: a macromolecular version of the Widom-Rowlinson model
gan: Addison, C, et al.
Cyhoeddwyd: (2005)