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Nucleic Acids Research, 2004, Vol. 32, Database issue D174-D181
© 2004 Oxford University Press

AANT: the Amino Acid–Nucleotide Interaction Database

Michael M. Hoffman1,2, Maksim A. Khrapov2, J. Colin Cox1, Jianchao Yao1, Lingnan Tong1,3 and Andrew D. Ellington*,1,2

1 Institute for Cellular and Molecular Biology, 2 Department of Chemistry and Biochemistry and 3 Department of Computer Sciences, University of Texas at Austin, Austin, TX 78712-0159, USA

*To whom correspondence should be addressed. Tel: +1 512 232 3424; Fax: +1 512 471 7014; Email: andy.ellington{at}mail.utexas.edu
Present address:
Michael M. Hoffman, EMBL—European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

We have created an Amino Acid–Nucleotide Interaction Database (AANT; http://aant.icmb.utexas. edu/) that categorizes all amino acid–nucleotide interactions from experimentally determined protein–nucleic acid structures, and provides users with a graphic interface for visualizing these interactions in aggregate. AANT accomplishes this by extracting individual amino acid–nucleotide interactions from structures in the Protein Data Bank, combining and superimposing these interactions into multiple structure files (e.g. 20 amino acids x 5 nucleotides) and grouping structurally similar interactions into more readily identifiable clusters. Using the Chime web browser plug-in, users can view 3D representations of the superimpositions and clusters. The unique collection and representation of data on amino acid–nucleotide interactions facilitates understanding the specificity of protein–nucleic acid interactions at a more fundamental level, and allows comparison of otherwise extremely disparate sets of structures. Moreover, by modularly representing the fundamental interactions that govern binding specificity it may prove possible to better engineer nucleic acid binding proteins.


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