Automatic annotation of BIND molecular interactions from three-dimensional structures

Biopolymers. 2001;61(2):111-20. doi: 10.1002/1097-0282(2001/2002)61:2<111::AID-BIP10143>3.0.CO;2-8.


Software to automate the process of extracting molecular interactions from three-dimensional (3D) structures has been developed that records these as Biomolecular Interaction Network Database (BIND) pairwise interaction records. Full annotation of BIND records is provided through a database processing tool called MMDBind, including detailed atom-atom and residue-residue level interaction information. BIND three-dimensional interaction annotation is synthesized by combining information from the Molecular Modeling Database (MMDB), and the HET (heterogen) group dictionary of small molecules in the macromolecular Crystallographic Information Format (mmCIF). Interactions are validated using the Protein Quaternary Structure (PQS) system. A total of 18,166 interactions were removed as being redundant or biologically irrelevant after PQS validation. This first pass MMDBind annotation creates two new divisions of BIND, 3D Biopolymers (BIND-3DBP) comprising 16,737 initial interaction records, and 3D Small Molecules (BIND-3DSM) comprising 48,219 records. Visualization of interacting residues and nucleotides within a macromolecular structure is possible directly from the BIND database owing to added 3D feature annotation within the BIND records that can be conveniently seen using Cn3D ("see-in-3D") after query from the BIND Data Manager. These interaction records provide a further demonstration of the completeness of the BIND data specification and its capabilities as storage and exchange format for all kinds of molecular interactions, including RNA, DNA, protein, and small molecules. Data from the 3DBP and 3DSM sets are available for downloading in Abstract Syntax Notation.1 (ASN.1) or Extensible Markup Language (XML) formats at Data from the 3DBP set is available for interactive query from the BIND Data Manager at

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • DNA / metabolism
  • Databases as Topic*
  • Internet
  • Models, Molecular
  • Protein Binding
  • Protein Structure, Quaternary
  • RNA / metabolism
  • Ribosomes / chemistry
  • Software*


  • RNA
  • DNA