title: SPRITE and ASSAM: web servers for side chain 3D-motif searching in protein structures.
abstract: Similarities in the 3D patterns of amino acid side chains can provide insights into their function despite the absence of any detectable sequence or fold similarities. Search for protein sites (SPRITE) and amino acid pattern search for substructures and motifs (ASSAM) are graph theoretical programs that can search for 3D amino side chain matches in protein structures, by representing the amino acid side chains as pseudo-atoms. The geometric relationship of the pseudo-atoms to each other as a pattern can be represented as a labeled graph where the pseudo-atoms are the graph's nodes while the edges are the inter-pseudo-atomic distances. Both programs require the input file to be in the PDB format. The objective of using SPRITE is to identify matches of side chains in a query structure to patterns with characterized function. In contrast, a 3D pattern of interest can be searched for existing occurrences in available PDB structures using ASSAM. Both programs are freely accessible without any login requirement. SPRITE is available at http://mfrlab.org/grafss/sprite/ while ASSAM can be accessed at http://mfrlab.org/grafss/assam/.
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: Eleanor J
authors.initials: EJ
authors.lastname: Gardiner
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: D020816:Amino Acid Motifs; D000596:Amino Acids / Q000737:chemistry; D019843:Archaeal Proteins / Q000737:chemistry; D001426:Bacterial Proteins / Q000737:chemistry; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D018272:Porins / Q000737:chemistry; D011487:Protein Conformation; D012984:Software
chemical_list: D000596:Amino Acids; D019843:Archaeal Proteins; D001426:Bacterial Proteins; D018272:Porins; C079242:ScrY protein, bacteria