oxDNA: coarse-grained simulations of nucleic acids made simple

[1]  M. Matthies,et al.  Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView , 2022, Nature Protocols.

[2]  P. Šulc,et al.  OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures , 2021, Nucleic Acids Res..

[3]  T. Ouldridge,et al.  A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results , 2021, Frontiers in Molecular Biosciences.

[4]  H. Su,et al.  Integrated computer-aided engineering and design for DNA assemblies , 2021, Nature Materials.

[5]  Nicolas Schabanel,et al.  ENSnano: A 3D Modeling Software for DNA Nanostructures , 2021, DNA.

[6]  Ivan Viola,et al.  Adenita: interactive 3D modelling and visualization of DNA nanostructures , 2020, Nucleic acids research.

[7]  David Doty,et al.  scadnano: A Browser-Based, Scriptable Tool for Designing DNA Nanostructures , 2020, DNA.

[8]  Christopher Maffeo,et al.  MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems , 2020, Nucleic acids research.

[9]  Michael Matthies,et al.  Design, optimization and analysis of large DNA and RNA nanostructures through interactive visualization, editing and molecular simulation , 2020, bioRxiv.

[10]  Lorenzo Rovigatti,et al.  TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami , 2019, J. Comput. Chem..

[11]  J. Marko,et al.  Twist-bend coupling and the statistical mechanics of DNA: perturbation theory and beyond , 2018, bioRxiv.

[12]  Tine Curk,et al.  Coarse-grained simulation of DNA using LAMMPS , 2018, The European physical journal. E, Soft matter.

[13]  Modesto Orozco,et al.  Multiscale simulation of DNA. , 2016, Current opinion in structural biology.

[14]  I. Z. Reguly,et al.  A comparison between parallelization approaches in molecular dynamics simulations on GPUs , 2014, J. Comput. Chem..

[15]  Flavio Romano,et al.  A nucleotide-level coarse-grained model of RNA. , 2014, The Journal of chemical physics.

[16]  Lorenzo Rovigatti,et al.  Coarse-graining DNA for simulations of DNA nanotechnology. , 2013, Physical chemistry chemical physics : PCCP.

[17]  Rosalind J Allen,et al.  Forward flux sampling for rare event simulations , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

[18]  Kevin E. Riley,et al.  Nature and magnitude of aromatic stacking of nucleic acid bases. , 2008, Physical chemistry chemical physics : PCCP.

[19]  M. Parrinello,et al.  Well-tempered metadynamics: a smoothly converging and tunable free-energy method. , 2008, Physical review letters.

[20]  S. Whitelam,et al.  Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles. , 2005, The Journal of chemical physics.

[21]  Y. Sugita,et al.  Replica-exchange molecular dynamics method for protein folding , 1999 .