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

Joakim Bohlin, Michael Matthies, Erik Poppleton, Jonah Procyk, Aatmik Mallya, Hao Yan, Petr Šulc

Published: 2022-06-05 DOI: 10.1038/s41596-022-00688-5

molecular dynamics

nanostructures

oxView

simulation

DNA/RNA design

AI 解读

Supplementary information

Supplementary Information

OxView and oxDNA file format description, scripting examples, ANM-oxDNA simulation setup, trajectory analysis and Listings S1-S17.

Supplementary Video 1

Importing and simulating nanostructures in oxView

Supplementary Video 2

Building hybrid DNA-protein system in oxView

Supplementary Data

Source codes of files for respective protocols, along with examples of expected outcomes

Efficient and safe single-cell cloning of human pluripotent stem cells using the CEPT cocktail

Profiling native pulmonary basement membrane stiffness using atomic force microscopy

Genetic circuit design automation with Cello 2.0

Synthesis of siRNA nanoparticles to silence plaque-destabilizing gene in atherosclerotic lesional macrophages

Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2)

A practical guide to scanning light-field microscopy with digital adaptive optics

Effective high-throughput isolation of fully human antibodies targeting infectious pathogens

Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments

MOF-derived nanoporous carbons with diverse tunable nanoarchitectures

Tutorial: a statistical genetics guide to identifying HLA alleles driving complex disease

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References

Supplementary information

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