title: IMAAAGINE: a webserver for searching hypothetical 3D amino acid side chain arrangements in the Protein Data Bank.
abstract: We describe a server that allows the interrogation of the Protein Data Bank for hypothetical 3D side chain patterns that are not limited to known patterns from existing 3D structures. A minimal side chain description allows a variety of side chain orientations to exist within the pattern, and generic side chain types such as acid, base and hydroxyl-containing can be additionally deployed in the search query. Moreover, only a subset of distances between the side chains need be specified. We illustrate these capabilities in case studies involving arginine stacks, serine-acid group arrangements and multiple catalytic triad-like configurations. The IMAAAGINE server can be accessed at http://mfrlab.org/grafss/imaaagine/.
authors.affiliation: School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia.
authors.forename: Nurul
authors.initials: N
authors.lastname: Nadzirin
authors.forename: Peter
authors.initials: P
authors.lastname: Willett
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Artymiuk
authors.forename: Mohd
authors.initials: M
authors.lastname: Firdaus-Raih
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D001120:Arginine / Q000737:chemistry; D020134:Catalytic Domain; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D012694:Serine / Q000737:chemistry; D012984:Software
chemical_list: D000596:Amino Acids; D012694:Serine; D001120:Arginine