DNAS

DNAS classifies local DNA conformations by assigning NTC: (Nucleotide Conformation) classes to dinucleotides extracted from DNA-containing structures to enable detailed analysis of DNA conformational variation.

Key Features:

• NTC assignment: Assigns NTC: (Nucleotide Conformation) classes to dinucleotides extracted from DNA-containing structures.
• DNA structural alphabet (NTA:): Implements the NTA: structural alphabet to group and represent patterns of dinucleotide NTC: classes.
• Algorithmic classification: Employs robust algorithms to perform the conformation-class assignments.
• Input format: Processes input structures in PDB format version 3.1 or above.
• Two-tier results: Produces two levels of results consisting of per-dinucleotide NTC: assignments and NTA:-based grouped annotations.
• Exportable data: Generates downloadable tables containing comprehensive assignment data for offline analysis.

Scientific Applications:

• Nucleic acid conformer analysis: Enables granular dinucleotide-level characterization of DNA conformers.
• Protein–DNA interface characterization: Provides detailed conformational information relevant to studies of protein/DNA interfaces.

Methodology:

Reads DNA-containing structures in PDB format version 3.1 or above, extracts dinucleotides, assigns NTC: (Nucleotide Conformation) classes using algorithmic classification, groups assigned classes into the NTA: structural alphabet, and outputs assignment tables.