Figure 6

Local environments of SeqFEATURE predictions for three TargetDB structures with unknown function. Three predicted functional sites from TargetDB structures are shown compared to known examples of the predicted function. The predicted and known sites are shown in yellow, positively charge atoms (nitrogens) are shown in blue, and negatively charged atoms (oxygens) are shown in red. Carbons and secondary structure are shown in grey. All atoms within 7.5 angstroms of the site are shown. (a) The active site of a known zinc protease (1KAP) is shown to the left of a zinc protease site in 2EJQ predicted by SeqFEATURE. Note the presence of two histidine residues (one can be seen clearly above each site) and a number of negative charges distributed throughout both local environments. Note also the similarity in secondary structure. (b) The local structure of 1FI6 (left), which contains a known EF hand calcium-binding motif, is compared to SeqFEATURE's predicted calcium-binding site in 2OGF. Note the similar distribution of negative charges and closely matching loop structures. The calcium is visible as a brown sphere in 1FI6, surrounded by oxygen atoms. (c) 1K8U is another known EF hand containing protein, shown to the left of the uncharacterized protein structure 2OX6, for which SeqFEATURE predicts calcium-binding. These figures were created using VMD [43].