ProNAB

ProNAB catalogs experimental binding affinities and thermodynamic parameters for protein–DNA and protein–RNA complexes to support analysis and modeling of protein–nucleic acid interactions.

Key Features:

• Extensive Data Collection: Houses over 20,000 experimental entries detailing binding affinities of protein–DNA and protein–RNA complexes derived from scientific literature.
• Comprehensive Information: Each entry includes sequence and structural features of proteins and nucleic acids, experimental conditions, and thermodynamic parameters: dissociation constants (Kd), binding free energy (ΔG), and changes in binding free energy upon mutation (ΔΔG).
• Integration with Existing Databases: Cross-links entries to GenBank, UniProt, PDB, ProThermDB, PROSITE, DisProt, and PubMed to connect genetic, structural, and functional information.

Scientific Applications:

• Analysis of affinity determinants: Enables analysis of sequence and structural determinants of binding affinity in protein–nucleic acid complexes.
• Predictive model development: Provides experimental binding and thermodynamic data for training and benchmarking computational models that predict binding affinities.
• Mutation impact assessment: Supports assessment and quantification of mutation-induced changes in binding free energy (ΔΔG).
• Rational design: Informs rational design and engineering of protein–nucleic acid interfaces with tailored affinities.

Methodology:

Data were collected from the scientific literature and cross-linked to GenBank, UniProt, PDB, ProThermDB, PROSITE, DisProt, and PubMed.