Iowa State University

Iowa State University

Protein-RNA Interface Database (PRIDB) v2.0

Dobbs and Honavar Laboratories

The Protein-RNA Interface Database (PRIDB) is designed to facilitate analyses of protein-RNA complexes. It provides in-depth information about existing PDB structures of protein-RNA complexes and their interfaces in an easy-to-access and machine-friendly format. PRIDB allows:

  • Detailed analyses of individual protein-RNA complexes and interfaces of interest
  • Rapid identification of interfacial residues in protein-RNA complexes
  • Extraction of atomic level information regarding interfacial contacts
  • Visualization of interfacial residues within the linear sequence of both protein & RNA chains
  • Visualization of interfacial residues in the context of the 3D structure of complexes
  • Identification of characterized motifs in protein (ProSite) or RNA (FR3D) chains
  • Generation of user-defined customized datasets of protein-RNA interfaces for statistical analyses and machine learning applications

PRIDB can be used to compute various statistics about any desired subset of structures (at the atomic, residue, or motif level), including such features as statistical binding propensity and interaction type propensity (e.g., the propensity of a glutamine residue to form a hydrogen bond with a guanine residue PRIDB's pre-generated datasets of protein-RNA interfaces can be used as benchmark datasets for comparing the performance of different interface prediction methods. PRIDB also facilitates the creation of customized datasets (e.g., a dataset containing only ribosomal protein-RNA complexes) for specific applications. PRIDB provides output in machine-readable format.

PRIDB Counts
Complexes and Chains Total Number in PRIDB Unique
Protein-RNA Complexes 1,484 1,484
Protein Chains 16,350 1,652
RNA Chains 3,398 1,110

Type Total (Interface + Non-interface) Number in Interfaces % in Interfaces
Amino Acids 2,772,451 1,071,874 38.7%
Ribonucleotides 1,312,999 741,900 56.5%

Please cite: Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant Honavar, and Drena Dobbs. PRIDB: A Protein-RNA Interface Database. Nucleic Acids Research 2010; doi: 10.1093/nar/gkq1108

Update log:

2011-07-20 - 271 new protein-RNA complexes added

2012-04-11 - 185 new protein-RNA complexes added

2013-03-26 - 76 new protein-RNA complexes added

2013-09-23 - Version 2.0 -- additional features added