Ab Initio Prediction of Transcription Factor Targets Using Structural Knowledge
Figure 3
Predicting the DNA Binding Site Motifs of Novel Transcription Factors
The protein's DNA-binding domains are identified using the Cys2His2 conserved pattern (top left). The residues at the key positions (6, 3, 2 and −1) of each finger (marked in red in the bottom left panel) are then assigned onto the canonical binding model (bottom right), and the sets of position-specific DNA-recognition preferences (top right panel) are used to construct a probabilistic model of the DNA binding site. For example, the lysine at the sixth position of the third finger faces the first position of the binding site (dotted blue arrow). We predict the nucleotide probabilities at this position using the appropriate recognition preferences (dotted black arrow).