DNA recognition by zinc finger proteins (ZFPs) plays an important role in gene regulation. However, the molecular determinants defining the recognition of specific DNA nucleotides by ZFP finger repeats has not yet been decoded. Here, we present a software that can predict:
(i) Which ZF repeats specifically bind to a DNA target sequence and
(ii) What is the most probable DNA target sequence for these repeats.

It can build and minimize a simple model of a ZFP/DNA complex by the given protein and DNA sequences, or by the predicted DNA. This procedure might take more than 1h.

Scoring matrix 1: scoring based on interactions of protein-DNA complexes
Scoring matrix 2: scoring based on interaction of ZFP-DNA complexes


Reference: Kalantzi et al., 2018