Nabe

Nabe catalogs experimentally determined amino acid mutations and their effects on binding free energy in protein-nucleic acid interactions to support analysis and prediction of binding-affinity changes.

Key Features:

• Comprehensive Mutation Data: Contains 2,506 mutations across 473 protein-nucleic acid complexes, including 1,751 alanine mutations in 405 complexes.
• Experimental Validation: Entries are derived from experimentally determined site-directed mutagenesis studies measuring effects on binding free energy in protein-DNA and protein-RNA complexes.
• Benchmark Databases: Integrates mutation data into benchmark databases using standardized data-processing procedures employed by predictive models.

Scientific Applications:

• Molecular mechanism analysis: Supports studies of transcription, translation, DNA replication, repair, recombination, RNA processing, and translocation by providing mutation-level binding free energy measurements.
• Predictive model development: Provides experimentally measured binding free energy changes for training, validating, and benchmarking computational algorithms that predict binding-affinity changes upon mutation.

Methodology:

Data were curated from site-directed mutagenesis experiments reported in the literature and processed using standardized data-processing procedures adopted for benchmark databases.