AANT: the Amino Acid-Nucleotide Interaction Database.
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.
Hoffman
Michael M
MM
Institute for Cellular and Molecular Biology, Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712-0159, USA.
Khrapov
Maksim A
MA
Cox
J Colin
JC
Yao
Jianchao
J
Tong
Lingnan
L
Ellington
Andrew D
AD
D000596:Amino Acids / Q000378:metabolism*; D000818:Animals; D001665:Binding Sites; D019295:Computational Biology; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D030541:Databases, Genetic; D006801:Humans; D020407:Internet; D008958:Models, Molecular; D009696:Nucleic Acids / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D009711:Nucleotides / Q000378:metabolism*; D011487:Protein Conformation; D012313:RNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software; D013379:Substrate Specificity
D000596:Amino Acids; D004268:DNA-Binding Proteins; D009696:Nucleic Acids; D009711:Nucleotides; D016601:RNA-Binding Proteins; D012313:RNA; D004247:DNA