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 (2024)  [Link]

Deep SNUPI

• Deep SNUPI is a graph neural network model that predicts the three-dimensional shape of DNA origami assemblies.

• GitHub  [Link]

• Graph neural network: Prediction of DNA origami shape using graph neural network, Nature Materials (2024)  [Link]