Fig. 2.

Example protein structure with bag of fragments and topic space representations; built for a given fragment library. (a) shows an example protein structure and (b) shows a given fragment library. Each substructure in protein is compared against the fragment library and the closest matching fragment is used to represent the substructure. Thus, we obtain bag of fragments representation for protein structure as shown in (c). We model the structure as a probability distribution over latent topics. In (d) we have shown a toy representation using three topics, which forms a simplex.