Fig. 5

Performance assessment of four methods using two well-known growth differentiation factors (GDF8, GDF11). As reported, the interaction between GDF8 and follistatin-288 (FS288) formed a protein complex to bind ‘heparin’, which defined the molecular mechanisms underlying GDF8’s key GO family: ‘heparin binding’ (GO:0008201) [52]. Different from GDF8, the varied residues in GDF11 made it unable to interact with FS288, and it therefore suffered from the loss of the ‘heparin binding’ function [53]. (a) Sequence alignment between GDF8 and GDF11, where varied residues between two GDFs were marked in light green and blue background, respectively. Three residue pairs (F315Y, V316M, and L318M on the binding surface between the GDF8 and FS288) which were found as key residue indicating GDFs’ ‘heparin binding’ function [55], were given in pink background. (b) Structure superimposition between GDF8 (light green) and GDF11 (blue) and their interactions with FS288 (gray surface). As highlighted in pink background, three residue pairs (F315Y, V316M, L318M) located in the binding interface between GDF and FS288. (c) function annotation results predicted by the methods. If a GO family is successfully predicted by a method, a colored circle would be adopted to indicate that prediction result. Particularly, a successful prediction made by AnnoPRO, NetGO3, PFmulDL or DeepGOPlus was indicated by a circle of light red, orange, light blue or light green, respectively. As described, AnnoPRO is the only one that can successfully predict all GO families for both GDFs