BindingDB: a web-accessible molecular recognition database

Comb Chem High Throughput Screen. 2001 Dec;4(8):719-25. doi: 10.2174/1386207013330670.


This paper presents an initial description of the BindingDB, a public web-accessible database of measured binding affinities for various molecular types ( The BindingDB allows queries based upon a range of criteria, including chemical similarity or substructure, sequence homology, numerical criteria (e.g. delta G(o) < 5 kcal/mol) and reactant names (e.g. "lysozyme"). Principles of Human-Computer Interactions are being employed in creating the query interface and user-feedback is being solicited. The data specification includes significant experimental detail. A full dictionary has been created for isothermal titration calorimetry data in consultation with experimentalists and data dictionaries for enzyme-inhibition and other measurement techniques are being developed. Currently, the BindingDB contains several data sets of broad interest, such as antigen-antibody binding and cyclodextrin/small molecule binding. However, it is anticipated that online deposition by experimentalists will ultimately contribute to a larger flow of data. We are actively developing software and file specifications to facilitate such deposition.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Binding Sites
  • DNA
  • Databases, Factual*
  • Guidelines as Topic
  • Proteins / metabolism
  • User-Computer Interface


  • Proteins
  • DNA