Local Function Conservation in Sequence and Structure Space
Figure 3
We exemplify the GOdot method on a set of five template proteins (t1–t5) having two different molecular functions (drawn in yellow and red, respectively). The training procedure (top row) consists of similarity calculations (A1), yielding four different similarity matrices one of which is shown (A2). Based on these similarities, logistic curves are fitted for each molecular function in the dataset (A3). The prediction (bottom row) comprises similarity computations between the query protein and the proteins in our dataset (B1), which are then used to predict the conservation of molecular functions in the queries proximity (B2). The final ranking of GO terms is obtained using combination schemes along the GO graph structure (B3). See Methods section for details.