Nanobase

Nanobase archives and provides access to DNA and RNA nanostructure designs to enable sharing, reuse, and computational analysis in nucleic acid nanotechnology.

Key Features:

• Data deposition: Accepts deposition of DNA and RNA nanostructure designs in various design formats.
• Search and retrieval: Provides search and browsing capabilities to locate and retrieve specific nanostructure entries.
• Metadata and visualization: Stores per-entry metadata including images, design files, optional 3D views, experimental data, protocols, and literature references.
• Design file conversion: Converts uploaded design files into oxDNA and PDB formats to support simulations, interactive editing, and 3D visualization.

Scientific Applications:

• Design sharing and reuse: Enables sharing and reuse of nucleic acid constructs across projects and research groups.
• Computational simulation and modeling: Supports setup of simulations and modeling workflows via conversion to oxDNA and PDB formats.
• Archival and reproducibility: Archives designs with associated experimental data, protocols, and literature to support reproducibility and experimental benchmarking.

Methodology:

Accepts various design formats, stores metadata and visualization data (images and optional 3D views), and provides conversion tools to generate oxDNA and PDB files alongside archived experimental data, protocols, and literature references.