ZIFIBI: Prediction of DNA binding sites for zinc finger proteins
Section snippets
Materials and methods
Construction of binding information (Position Weighted Matrix). To quantify the interaction between the 3 nucleotides and amino acids in positions −1, 3, and 6 of the C2H2 zinc finger domain [7], we searched publically available data for zinc finger binding sites and found 187 C2H2 zinc finger domains verified by previous biochemical experiments [11], [12], [13], [14]. These C2H2 domains could potentially interact with 45 different combinations of 3 bp long nucleotide sequences.
Using the
Results
To predict the DNA binding site of the C2H2 zinc finger domain, we obtained specific amino acid sequences from SWISS-PROT for 1108 proteins that contain more than two C2H2 zinc finger domains [16]. We used the C2H2 conserved pattern (C–X(2–5)–C–X(3)–(F/Y/)–X(8)–H–X(3–5)–H) of 952 of the proteins for the identification of amino acids in positions −1, 3, and 6 in the C2H2 zinc finger domain [17], [18]. It was not possible to identify the amino acids in 156 of the proteins because they did not
Discussion
The ZIFIBI database we created contains proteins with potential binding sites for zinc finger proteins that have not yet been experimentally identified. We compared ZIFIBI with three other studies in which DNA binding site predictions for C2H2 zinc finger domains were made. TRANSFAC, one of the databases used for comparison, includes 28 binding matrices for C2H2 zinc finger proteins. The average Euclidean distance of ZIFIBI was 0.613929, which is lower than those found in other studies
Web interfaces
ZIFIBI provides DNA binding site information for C2H2 zinc finger proteins and provides convenient computational methods to search for target genes.
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Function to search DNA binding sites: ZIFIBI has a searching function by gene name, SWISS-PROT ID or SWISS-PROT access number for specific protein.
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Function to search target genes: ZIFIBI has target gene list for C2H2 zinc finger proteins and binding sites in the 2.1 kb promoter region of target gene.
ZIFIBI provides information that will further our
Acknowledgment
This work was supported in part by Ministry of Science and Technology (MOST) Grants (M10411010001-06O1101-00110).
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Cited by (0)
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Present address: DNA Link Inc., Seoul, Republic of Korea.
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Present address: Korean Bioinformation Center, KRIBB, Republic of Korea.