Protein Meta-Functional Signatures from Combining Sequence, Structure, Evolution, and Amino Acid Property Information
Figure 3
The different predictive performance of the MFS method, the SeqonlyMFS method, the Evolutionary Trace server, and the ConSurf server on two examples.
The structure of an ornithine decarboxylase (A) (PDB identifier 1ord-A) and a cellobiohydrolase (B) (PDB identifier 1cel-A) are shown in the ribbon representations with the functional sites (223H-316D-355K in 1ord-A, 212E-214D-217E-228H in 1cel-A) represented as spheres. Each residue is colored by its predicted functional importance score, with the color changing from red to white to blue as the score decreases. For 1ord-A (A), both MFS and SeqonlyMFS work well in assigning the highest scores to the functional sites. However, ET and ConSurf also assign high scores to nearby residues in the surrounding cavity, thus the functional sites do not appear in the top-10 hits lists that are generated by these methods. For 1cel-A (B), all the sequence-based methods are able to assign relatively high scores to the functional sites (different shades of red color), but only the MFS method that uses structural information can boost the scores of the functional sites higher (more intense red color) to show up in the top-10 hits list.