Fig. 1

Approaches for predicting binding specificities in zinc finger protein. a Pipelines for the three approaches. Prediction of the optimal ZFP for a unique address in the genome is made by searching in the space of Zif-268 mutants in all these approaches. b DNA Targets: Approach 1 assumes modular mode of binding and a negative binder is used as the control for generating all 64 DNA targets (N = A/T/G/C); Approach 2 assumes synergistic mode of binding and a negative binder is used both as the control and the flanking unit across the repeating triplets of all possible 16 GNN DNA targets; Approach 3 assumes modular mode of binding and the wild type DNA is used as a control for generating all 64 DNA targets. c Mutations introduced in the key residues positions of the Zif-268 α-helix: Approach 1 incorporates the consensus amino acid framework as reported by Isalan et al. 1998. [20]; Apart from the mutations introduced in Approach 1, for Approach 2, glutamic acid (E) was introduced at position 3 as well; Approach 3 introduces all 20 amino acids as possibilities at all three positions