Nucleic Acid Database (NDB)

Nucleic Acid Database (NDB) curates and manages experimentally determined three-dimensional DNA and RNA structures by integrating primary crystallographic information and derived structural parameters to support structural analysis of nucleic acids.

Key Features:

• Relational storage: Relational database storing primary crystallographic information and derived structural parameters for DNA and RNA models.
• Data ingestion and validation: Encoding and validating primary experimental data from literature, PDB files, CIF archives, and crystallographic software outputs.
• Format translation: Translating data between NDB, PDB, and CIF formats.
• Schema and SQL generation: Generating relational schemas and ANSI-SQL database representations.
• Derived metric computation: Computing derived structural metrics including bond geometries, torsion angles, virtual phosphate parameters, and base morphology descriptors.
• Sequence–structure integration: Integrating nucleic acid sequence data with high-resolution structural features.
• Conformational descriptors: Computing and representing conformation rings and base morphology descriptors for conformational analysis.
• Querying and reporting: Constructing customizable reports and enabling queries using both primary and derived structural features.
• External tool interfacing: Interfacing with external analysis tools such as Dials and Windows or local 3D molecular visualization software.
• Archival computation: Preparing archival data and automating computation of structural descriptors across stored DNA and RNA models to support reproducible research.

Scientific Applications:

• Conformational analysis: Analysis of nucleic acid conformation using torsion angles, bond geometries, conformation rings, and base morphology descriptors.
• Interaction and recognition studies: Investigation of nucleic acid interactions and protein recognition mechanisms.
• Comparative structural analysis: Retrieval and comparison of structural features across DNA and RNA models.
• Archival and deposition: Preparation and translation of archival data for deposition and dissemination using NDB, PDB, and CIF formats.
• Large-scale structural studies: Support for large-scale structural studies aligned with high-throughput sequencing and crystallographic technologies.

Methodology:

Encoding and validating experimental data from literature, PDB files, CIF archives, and crystallographic software outputs; translating between NDB, PDB, and CIF formats; generating relational schemas and ANSI-SQL representations; computing derived structural metrics including bond geometries, torsion angles, virtual phosphate parameters, and base morphology descriptors.