BindingDB: a web-accessible molecular recognition database.
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. 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.
Chen
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Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, MD 20850, USA. chen@umbi.umd.edu
Liu
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Gilson
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MK
D001665:Binding Sites; D004247:DNA; D016208:Databases, Factual; D017408:Guidelines as Topic; D011506:Proteins / Q000378:metabolism; D014584:User-Computer Interface
D011506:Proteins; D004247:DNA