A coarse-grained model for DNA origami

Structure and conformational dynamics of scaffolded DNA origami nanoparticles

(2017) Keyao Pan et al.   NUCLEIC ACIDS RESEARCH

Direct Simulation of the Self-Assembly of a Small DNA Origami

(2016) Benedict E. K. Snodin et al.   ACS Nano

Enhancing Important Fluctuations: Rare Events and Metadynamics from a Conceptual Viewpoint

(2016) Omar Valsson et al.   Annual Review of Physical Chemistry

De novoreconstruction of DNA origami structures through atomistic molecular dynamics simulation

(2016) Christopher Maffeo et al.   NUCLEIC ACIDS RESEARCH

Designer nanoscale DNA assemblies programmed from the top down

(2016) R. Veneziano et al.   SCIENCE

SIRAH: A Structurally Unbiased Coarse-Grained Force Field for Proteins with Aqueous Solvation and Long-Range Electrostatics

(2015) Leonardo Darré et al.   Journal of Chemical Theory and Computation

Martini Coarse-Grained Force Field: Extension to DNA

(2015) Jaakko J. Uusitalo et al.   Journal of Chemical Theory and Computation

DNA rendering of polyhedral meshes at the nanoscale

(2015) Erik Benson et al.   NATURE

Designer three-dimensional DNA architectures

(2014) Yonggang Ke   CURRENT OPINION IN STRUCTURAL BIOLOGY

Functional Analysis of Drosophila HSP70 Promoter with Different HSE Numbers in Human Cells

(2014) Nadezda Kust et al.   PLoS One

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

(2013) Thomas E. Ouldridge et al.   NUCLEIC ACIDS RESEARCH

Sequence-dependent thermodynamics of a coarse-grained DNA model

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

Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA

(2012) Miroslav Krepl et al.   Journal of Chemical Theory and Computation

Modeling the mechanical properties of DNA nanostructures

(2012) Jean Michel Arbona et al.   PHYSICAL REVIEW E

Cryo-EM structure of a 3D DNA-origami object

(2012) X.-c. Bai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Logic-Gated Nanorobot for Targeted Transport of Molecular Payloads

(2012) S. M. Douglas et al.   SCIENCE

Recent successes in coarse-grained modeling of DNA

(2012) Davit A. Potoyan et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

A primer to scaffolded DNA origami

(2011) Carlos Ernesto Castro et al.   NATURE METHODS

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

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

A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics

(2010) Pablo D. Dans et al.   Journal of Chemical Theory and Computation

Self-assembly of DNA into nanoscale three-dimensional shapes

(2009) Shawn M. Douglas et al.   NATURE

Rapid prototyping of 3D DNA-origami shapes with caDNAno

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

UNIQUIMER 3D, a software system for structural DNA nanotechnology design, analysis and evaluation

(2009) J. Zhu et al.   NUCLEIC ACIDS RESEARCH

DNA Origami Design of Dolphin-Shaped Structures with Flexible Tails

(2008) Ebbe S. Andersen et al.   ACS Nano