Title: BindingDB: A Web-Accessible Molecular Recognition Database
VOLUME: 4 ISSUE: 8
Author(s):Xi Chen, Ming Liu and Michael K. Gilson
Affiliation:Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, MD, 20850, USA
Keywords:Simplified molecular input line entry specification
Abstract: This paper presents an initial description of the BindingDB, a public web-accessible database of measured binding affinities for various molecular types (http://www.bindingdb.org). The BindingDB allows queries based upon a range of criteria, including chemical similarity or substructure, sequence homology, numerical criteria (e.g. DeltaGo < 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 a larger flow of data. We are actively developing software and file specifications to facilitate such deposition.
