How to use the BANMOKI database

Using the database

Overview The front page of the BANMOKI database displays short description of content and offers users three further options to explore by hitting one out of three buttons located on the top and on the bottom of the page. For better visual perception a button is highlighted and the text on it changes color when mouse pointer is on the button. The first choice is to browse the whole content of the database and full information for each individual entry (the Browse full content button). The second option is to search the content with respect to variety of parameters and browse through the search results (the Search database button). There is also an opportunity to send the creators of the database comments and suggestions about improving the database (the Send a comment button). This last part is protected against spammers on programming level by disallowing any kind of commercials.

Browsing the database. When Browse button on the front page is hit, the user is offered a choice which of five of the NMPK families will be displayed further. Besides the buttons for choosing the family links are provided to the plain text files containing multiple sequence alignments and annotation of functional important sites for the particular family. After choosing the family a screen with a portion of content for that particular family is displayed with links to plain text files containing following information for each individual entry:
         1. Sequence in the FASTA format;
         2. Results of the Psi-Blast search for this sequence;
         3. PDB file of a model structure;
         4. Total pKa's for all titratable residues in the model;
         5. Intrinsic pKa's for all titratable residues in the model ;
         6. pH dependence of the net charge for the model.
For user convenience each screen displays only 10 entries with easy navigation links at the bottom and top of the page. Each information file is downloadable and PDB file of a model can be directly viewed in any PDB viewer if Internet browser is configured properly.

Searching the database. We 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. For better visual perception of the search screen, the name of a search criterion is blurred and the related fields are disabled when this criterion is not selected. For the numerical inquiries, the user is given a choice to search for values exactly equal to (with 5% tolerance level), larger than, smaller than, or between the desired value(s) (in the last case, the additional field appears in the screen for upper threshold of the value).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. Search results table contains minimum relevant information such as sequence ID, name of the protein, family to which the protein belongs, as well as total number of residues and number of titratable residues. User can download all or part of the search results as a single gzipped archive file by checking corresponding boxes in the left portion of the screen. If a user is interested in exploring further a particular entry, a link is provided to obtain the full information for this entry. The full-information screen in this case contains values of total pKa and its components calculated for each titratable residue of a given protein using three-dimensional structure of homology-build model.