dbAMEPNI: A database of Alanine Mutagenic Effects for Protein-Nucleic Acid Interactions


A web-based and searchable database of alanine-scanning mutations and their effects on the binding affinity of protein-nucleic acid interactions. The molecular types of nucleic acids can be classified into five major categories: a hybrid of DNA/RNA, dsDNA (double-stranded DNA), ssRNA (single-stranded RNA), ssDNA (single-stranded DNA), and dsRNA (double-stranded RNA). dbAMEPNI is a manually curated, literature-derived database, focusing on the effects of single alanine-scanning mutations on the binding affinities of protein-nucleic acid interfaces. As of November 2017, it comprises a total of 859 alanine-scanning mutant residues with quantitative or qualitative data in the change on binding affinity (details shown in below), extracted from 217 protein-nucleic acids complexes with three dimensional structures, which are deposited in Protein Data Bank (PDB). The database not only provides a benchmark dataset for developing efficient computational methods to predict unknown hotspots (i.e., ΔΔG >= 2.0 kcal/mol) on protein-nucleic acid interfaces, but also will be benefit for studying the principal rules governing protein-nucleic acids interactions.

If you used our database, please cite: L. Liu, Y. Xiong, H. Gao, D.Q. Wei, J.C. Mitchell and X. Zhu dbAMEPNI: a database of alanine mutagenic effects for protein–nucleic acid interactions. DATABASE-The Journal of Biological Databases and Curation 2018; Doi: 10.1093/database/bay034

Statistics of latest release (Last update: November 30, 2017):

All Entries 859
Core Set: Entries of Alanine-scanning Mutants with Quantitative Change Data in the Free Energy of Binding (ΔΔG) 577
 (Hotspots: Entries of Alanine-scanning Mutants with ΔΔG >= 2.0 kcal/mol  133)
Extended Set: Entries of Alanine-scanning Mutants without Quantitative Change Data but with Qualitative Data (or Descriptive Effects) 282

Related Links :

  • ASEdb: a searchable database of single alanine mutations in protein–protein, protein–nucleic acid, and protein–small molecule interactions for which binding affinities have been experimentally determined.

  • PROXiMATE: a mutant protein-protein interaction kinetics and thermodynamics database for mutant protein heterodimer complexes collected from literature and previously published databases.

  • Platinum: a database comprising over 1000 mutations, associates for the first time experimental information on changes in affinity with three-dimensional structures of protein–ligand complexes.

  • ProNIT: thermodynamic databases of experimentally determined thermodynamic parameters of protein–nucleic acid interactions.