protNAff

protNAff extracts and analyzes nucleic acid fragments from 3D structures to produce context-specific fragment libraries and searchable databases for quantitative studies of RNA conformation and protein–RNA interactions.

Key Features:

• Modular Pipeline Design: Enables customization for specific modeling problems.
• Context-Specific Filtering: Generates searchable databases with filters for specific nucleic acid regions or structures.
• Fragment Library Creation: Constructs tailored libraries of protein-bound RNA fragments from 3D structural data.

Scientific Applications:

• Trinucleotide conformation analysis: Performs quantitative analysis of sequence-specific trinucleotide conformations using fragments from 3D structures.
• RNA conformational diversity assessment: Examines conformational diversity in RNA at multiple levels.
• Protein-binding impact on RNA conformation: Investigates effects of protein binding on local RNA conformations using protein-bound fragments.
• Hairpin loop protein-binding propensity: Analyzes hairpin loops' propensity to bind proteins across various loop lengths.

Methodology:

Extracts nucleic acid fragments from 3D structures in the Protein Data Bank (PDB) and analyzes those structural contexts to build comprehensive, searchable databases; the modular pipeline applies filters for specific nucleic acid regions or structures to create tailored fragment libraries.