Design and simulation of DNA, RNA and hybrid protein–nucleic acid nanostructures with oxView

Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution

(2021) Jae Young Lee et al.   ACS Nano

Absolute and arbitrary orientation of single-molecule shapes

(2021) Ashwin Gopinath et al.   SCIENCE

The Art of Designing DNA Nanostructures with CAD Software

(2021) Martin Glaser et al.   MOLECULES

Integrated computer-aided engineering and design for DNA assemblies

(2021) Chao-Min Huang et al.   NATURE MATERIALS

Strategies for Constructing and Operating DNA Origami Linear Actuators

(2021) Erik Benson et al.   Small

Clustering of Death Receptor for Apoptosis Using Nanoscale Patterns of Peptides

(2021) Yang Wang et al.   ACS Nano

DNA Origami Penetration in Cell Spheroid Tissue Models is Enhanced by Wireframe Design

(2021) Yang Wang et al.   ADVANCED MATERIALS

A Self-Regulating DNA Rotaxane Linear Actuator Driven by Chemical Energy

(2021) Ze Yu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results

(2021) A. Sengar et al.   Frontiers in Molecular Biosciences

Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels

(2020) Ye Tian et al.   NATURE MATERIALS

MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems

(2020) Christopher Maffeo et al.   NUCLEIC ACIDS RESEARCH

Adenita: interactive 3D modelling and visualization of DNA nanostructures

(2020) Elisa de Llano et al.   NUCLEIC ACIDS RESEARCH

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Meta-DNA structures

(2020) Guangbao Yao et al.   Nature Chemistry

Understanding DNA interactions in crowded environments with a coarse-grained model

(2020) Fan Hong et al.   NUCLEIC ACIDS RESEARCH

Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution

(2020) Massimo Kube et al.   Nature Communications

Tunable Nanoscale Cages from Self-Assembling DNA and Protein Building Blocks

(2019) Yang Xu et al.   ACS Nano

TacoxDNA: A user‐friendly web server for simulations of complex DNA structures, from single strands to origami

(2019) Antonio Suma et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Computer-Aided Production of Scaffolded DNA Nanostructures from Flat Sheet Meshes

(2016) Erik Benson et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

(2015) Benedict E. K. Snodin et al.   JOURNAL OF CHEMICAL PHYSICS

DNA rendering of polyhedral meshes at the nanoscale

(2015) Erik Benson et al.   NATURE

A nucleotide-level coarse-grained model of RNA

(2014) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

A comparison between parallelization approaches in molecular dynamics simulations on GPUs

(2014) Lorenzo Rovigatti et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Coarse-graining DNA for simulations of DNA nanotechnology

(2013) Jonathan P. K. Doye et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Sequence-dependent thermodynamics of a coarse-grained DNA model

(2012) Petr Šulc et al.   JOURNAL OF CHEMICAL PHYSICS

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

(2011) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

Challenges and opportunities for structural DNA nanotechnology

(2011) Andre V. Pinheiro et al.   Nature Nanotechnology

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures

(2011) Do-Nyun Kim et al.   NUCLEIC ACIDS RESEARCH

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Rapid prototyping of 3D DNA-origami shapes with caDNAno

(2009) Shawn M. Douglas et al.   NUCLEIC ACIDS RESEARCH

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY