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Showing search results (1–2 of 2):

  1. BANMOKI
    Full Name of the Resource : Database of bacterial nucleoside monophosphate kinases
    Resource Category : Databases -> Protein Sequence Databases -> Databases of individual protein families

    Brief Description : 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.
    Subject Area : Protein Structure


    Institute/s :
    Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson,USA
    Address of Institute/s :
    Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA

    Country : USA; Bulgaria

    Associated Institutes :

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

    Associated Country : USA; Bulgaria


    Authors/Contributors : Kundrotas P J; Georgieva P; Shosheva A; Christova P; Alexov E
    Contact Email : pkundro@clemson.edu
    Year : 2007
    Language : English

    Keywords : Bacteria enzymology genetics; Biophysical Phenomena; Biophysics; Computer Simulation; Databases, Protein; Internet; Models, Molecular; Nucleoside-Phosphate Kinase chemistry genetics; Sequence Alignment; Static Electricity


  2. BANMOKI (View Publication)
    Full Name of the Resource : Database of bacterial nucleoside monophosphate kinases
    Resource Category : Databases -> Protein Sequence Databases -> Databases of Individual Protein Families

    Brief Description : 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.
    Subject Area : Bacterial Nucleoside Monophasphate Kinase


    Institute/s :
    Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
    Address of Institute/s :
    Computational Biophysics and Bioinformatics, Department of Physics, Clemson University, Clemson, SC 29634, USA
    Country : United States

    Associated Institutes :

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

    Associated Country : USA; Bulgaria


    Authors/Contributors : Kundrotas P.J.
    Contact Email : pkundro@clemson.edu
    Year : 2007
    Language : English

    Keywords : Bacteria / enzymology / genetics; Biophysical Phenomena; Biophysics; Computer Simulation; Databases, Protein; Internet; Models, Molecular; Nucleoside-Phosphate Kinase / chemistry / genetics; Sequence Alignment; Static Electricity