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.
Keywords: Simplified molecular input line entry specification
Combinatorial Chemistry & High Throughput Screening
Title: BindingDB: A Web-Accessible Molecular Recognition Database
Volume: 4 Issue: 8
Author(s): Xi Chen, Ming Liu and Michael K. Gilson
Affiliation:
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.
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Cite this article as:
Chen Xi, Liu Ming and Gilson K. Michael, BindingDB: A Web-Accessible Molecular Recognition Database, Combinatorial Chemistry & High Throughput Screening 2001; 4 (8) . https://dx.doi.org/10.2174/1386207013330670
DOI https://dx.doi.org/10.2174/1386207013330670 |
Print ISSN 1386-2073 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5402 |
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