MotiveQuery: Language and Web Service for Fast Identification of Protein Structural Motifs in the Entire Protein Data Bank

illustrate the usefulness of MQ, we provide a case study for sugar binding sites in proteins of gram-negative bacteria. The protein PA-IIL is one of the virulent factors of the Pseudomonas aeruginosa, as it aids this pathogen in host recognition by recognizing the sugars which coat the surface of the host cell. The sugar binding site of PA-IIL contains two close calcium cations that mediate the binding of the sugar. These cations are coordinated by seven amino acids. We attempted to identify all binding sites that could function similarly to the PA-IIL sugar binding site. In order to do so, we defined the PA-IIL sugar binding site using MQ. The whole process comprised of several simple individual tasks: Case study-gram-negative bacteria sugar binding site • BLOCKINAtoms(" Ca ")-Select calcium atoms • BLOCKINCluster(4,Atoms(" Ca "))-Create a motif made of calcium atoms which are closer than 4Å.