NAR Molecular Biology Database Collection entry number 976

http://www.ces.clemson.edu/compbio/databases/kinases

Kundrotas P.J.¹, Georgieva P.², Shosheva A.³, Christova P.³ and Alexov E.¹

¹Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
²Institute of Organic Chemistry, Bulgarian Academy of Sciences, Sofia-1113, Bulgaria
³Institute of Biophysics, Bulgarian Academy of Sciences, Sofia-1113, Bulgaria

Contact pkundro@clemson.edu

The database of BActerial Nucleoside MOnophosphate KInases (BANMOKI) is a collection of homology-based models of three-dimensional structures of all five bacterial nucleoside monophosphate kinases (NMPK) families, their pre-computed properties and other relevant information. Each entry in the database contains the following information sequence identity, PDB file of 3D model structure, Enzyme Commission (EC) number, pKa values of all titratable groups, desolvation penalty, interaction energy with permanent dipoles and the net charge of folded and unfolded states as a function of pH. We also have implemented a search engine using combination of CGI Perl programs and embedded Java scripts. User can search either within the whole database or within the particular family with respect of any combination of the following parameters: name, sequence ID, values of pKa and its components. An option to download all or part of the search results is also available. Users are given a choice of searching for values exactly equal to (with 5% tolerance level), larger than, smaller than or between desired value(s). The search results can then be sorted in ascending or descending order by any of searchable parameters. Users can also choose either AND or OR conjunction between the search criteria.

The database is currently being updated to include the new sequences and to take advantage of the new available templates and is currently upgraded to include the models of the post reaction (holo) form of all family members.

The web server development and the corresponding scientific work was supported by NATO collaborative grant CBP.EAP.CLG 981749.

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