The Dataset for protein-RNA Binding Affinity

Protein Sci. 2013 Dec;22(12):1808-11. doi: 10.1002/pro.2383.

Abstract

We have developed a non-redundant protein-RNA binding benchmark dataset derived from the available protein-RNA structures in the Protein Database Bank. It consists of 73 complexes with measured binding affinity. The experimental conditions (pH and temperature) for binding affinity measurements are also listed in our dataset. This binding affinity dataset can be used to compare and develop protein-RNA scoring functions. The predicted binding free energy of the 73 complexes from three available scoring functions for protein-RNA docking has a low correlation with the binding Gibbs free energy calculated from Kd.

Keywords: binding affinity benchmark; binding free energy; protein-RNA docking; scoring function.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Computer Simulation
  • Crystallography, X-Ray
  • Data Collection*
  • Databases, Protein
  • Molecular Docking Simulation
  • Protein Binding
  • Proteins / chemistry
  • Proteins / metabolism*
  • Proteomics
  • RNA / metabolism*
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism*
  • Thermodynamics

Substances

  • Proteins
  • RNA-Binding Proteins
  • RNA