The Nucleic Acid Knowledgebase: a new portal for 3D structural information about nucleic acids

Area of Science:

• Structural Biology
• Bioinformatics
• Molecular Biology

Background:

• The Nucleic Acid Database (NDB) was a key resource for experimentally determined 3D nucleic acid structures.
• There was a need for a successor to the NDB with updated content and enhanced functionality.
• Access to comprehensive and well-annotated nucleic acid structure data is crucial for biological research.

Purpose of the Study:

• To introduce the Nucleic Acid Knowledgebase (NAKB) as a new, comprehensive data resource for nucleic acid structures.
• To provide a successor to the NDB, preserving its functionality while adding novel features.
• To facilitate the exploration and analysis of DNA and RNA 3D structures and their biological assemblies.

Main Methods:

• Indexing experimentally determined 3D structures of DNA and RNA polymers and biological assemblies.
• Integrating data from major structure determination methods including X-ray, NMR, and EM.
• Incorporating all structures from the Protein Data Bank (PDB) relevant to nucleic acids.
• Developing custom interactive tools for data exploration and analysis.

Main Results:

• NAKB is a new data resource, updated weekly, containing experimentally determined 3D nucleic acid structures.
• It includes structures from X-ray, NMR, and EM, and all relevant PDB entries.
• NAKB preserves NDB functionality and adds novel nucleic acid-centric content, including annotations and external links.
• Custom interactive tools are available for rapid data exploration.

Conclusions:

• NAKB serves as a vital, up-to-date resource for researchers studying nucleic acid structures.
• Its comprehensive data and advanced tools support deeper understanding of DNA and RNA biological functions.
• NAKB is positioned to be the leading platform for nucleic acid structural information.