title: BANMOKI: a searchable database of homology-based 3D models and their electrostatic properties of five bacterial nucleoside monophosphate kinase families.
abstract: The nucleoside monophosphate kinases (NMPK) are important enzymes that control the ratio of mono- and di-phosphate nucleosides and participate in gene regulation and signal transduction in the cell. However, despite their importance only several 3D structures were experimentally determined in contrast to the wealth of sequences available for each of the NMPK families. To fill this gap we present a Web-based database containing structural models for all proteins of the five bacterial nucleoside monophosphate kinase (bNMPK) families. The models were computed by means of homology-based approach using a few experimentally determined bNMPK structures. The database also contains pK(a) values and their components calculated for the homology-based 3D models, which is a unique feature of the database. The BActerial Nucleoside MOnophosphate KInases (BANMOKI) database is freely accessible (http://www.ces.clemson.edu/compbio/banmoki) and offers an easy user-friendly interface for browsing, searching and downloading content of the database. The users can investigate, using the searching tools of the database, the properties of the bNMP kinases in respect to sequence composition, electrostatic interactions and structural differences.
authors.affiliation: Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29642, USA.
authors.forename: Petras
authors.initials: P
authors.lastname: Kundrotas
authors.forename: Paulina
authors.initials: P
authors.lastname: Georgieva
authors.forename: Alexandra
authors.initials: A
authors.lastname: Shosheva
authors.forename: Petya
authors.initials: P
authors.lastname: Christova
authors.forename: Emil
authors.initials: E
authors.lastname: Alexov
mesh_terms: D001419:Bacteria / Q000201:enzymology* / Q000235:genetics; D055592:Biophysical Phenomena; D001703:Biophysics; D003198:Computer Simulation; D030562:Databases, Protein; D020407:Internet; D008958:Models, Molecular; D009703:Nucleoside-Phosphate Kinase / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D055672:Static Electricity
chemical_list: D009703:Nucleoside-Phosphate Kinase