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Domain Analysis

Protein sequences are input using one-letter amino acid codes. Any other non-standard symbols, spaces, or special characters are ignored.
For an input protein, the online program will locate the zinc fingers in your protein sequence and output the predicted 3bp DNA target for each zinc finger domain using our Nearest Neighbor predicor.

Target Analysis

For a desired 3bp DNA target, we provide a list of domains found in our data that we expect to bind that target in either the F2 or F3 positions, along with their inferred binding specificities. You may select the 3bp DNA target and the desired finger position (F2 or F3).

Experimental Database Download

Each file contains the set of helices observed to bind the given target, along with the logged and normalized frequency with which is was observed in the sequencing data. These helices are specified by the amino acids in the -1, 1, 2, 3, 5, and 6 positions.

Terms of Use

These data files are free of all copyright restrictions and made fully and freely available for non-commercial purposes. If you use these data, results, or our online prediction program in your publication, we request that you please cite the following papers:

Contact us

To give feedback or to send your comments or suggestions please email us: persikov at