Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures
Fig 3
Examples of SmotifTF predictions in the benchmark test set.
The structural superposition of the top-scoring model (pink cartoon) with the native structure (green cartoon) is shown in the middle. The proteins that provide the Smotif fragments to the top-scoring model are shown in grey cartoon, with the Smotif themselves colored according to the secondary structure elements present in them (helix = red, strand = yellow, loop = green). The PDB id, chain id and residue numbers of the Smotif fragments are shown along with the root mean square deviation (RMSD) of the respective Smotif fragments compared to the corresponding native Smotif. The SCOP ids of the proteins are provided, where available. (a) N-terminal domain of a protein with unknown function from Vibrio Cholerae (PDB: 4ro3A) (b) RNA binding protein Tho1 from Saccharomyces Cerevisiae (PDB: 4uzxA) (c) Mammalian Endoribonuclease Dicer (PDB: 4wyqA).