SNUPI (Structured NUcleic-acids Programming Interface)
SNUPI is a multiscale analysis framework based on the finite element model with the intrinsic properties of DNA characterized by molecular dynamics simulations.
GitHub [Link]
Technical details
- SNUPI framework (static analysis): Rapid computational analysis of DNA origami assemblies at near-atomic resolution, ACS Nano (2021), [Link]
- Improved model of single-stranded DNA: Characterizing and harnessing the mechanical properties of short single-stranded DNA in structured assemblies, ACS Nano (2021), [Link]
- Partition and relocation framework (free-form structures): Predicting the free-form shape of structured DNA assemblies from their lattice-based design blueprint, ACS Nano (2022), [Link]
- Langevin dynamics simulations: A computational model for structural dynamics and reconfiguration of DNA assemblies, Nature Communications (2023), [Link]
- EtBr-binding simulations: Predicting the effect of binding molecules on the shape and mechanical properties of structured DNA assemblies, Nature Communications (2023), [Link]
Deep SNUPI
Deep SNUPI is a graph neural network model that predicts the three-dimensional shape of DNA origami assemblies. It was trained by a hybrid data-driven and physics-informed approach.
GitHub [Link]
Technical details
- Graph neural network: Prediction of DNA origami shape using graph neural network, Nature Materials (2024), [Link]