DNA nanotechnology

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DNA Origami Structure Prediction

This service performs a series of brief coarse-grained simulations of a DNA origami object, first at low resolution to produce rapid relaxation of a structure, then at high-resolution to enable mapping to an atomistic structure.

Converting caDNAno design JSON file to all-atom PDB file

CaDNAno is a software with graphical interface for designing DNA origami. This service converts caDNAno designs in JSON format to atomic models suitable for 3D visualization.

Converting NanoEngineer-1 DNA structure design (MMP file) to all-atom PDB file

NanoEngineer-1 is a popular software package for designing arbitrary DNA nanostructures in a 3D workspace. Here we provide a service that converts a DNA nanostructure in NanoEngineer-1 (MMP format) to an all-atom structure in PDB format. It also generates files suitable for all-atom simulation.

ENRG MD for Origami Structure Prediction

DNA origami is a cost-effective method of assembling nanoscale objects by folding a long DNA strand using a custom set of complementary strands. Experimental characterization of DNA origami structure is essential for accurate design, but has been limited to rather low-resolution techniques. We developed a protocol that predicts DNA origami structure at atomic resolution with high accuracy using modest computational resources. Here we provide a service that prepares configuration files for a DNA origami structure prediction simulation from a caDNAno design file.