|-||Microsoft .NET Framework should be installed first to run PRI-Modeler.|
For the analysis of base pairs, PRI-Modeler takes a single PDB as input. For the analysis of protein-RNA interactions, PRI-Modeler takes one or more PDB files as input, and analyzes the protein-RNA interactions in all the PDB files.
Load PDB file(s) Menu:
A dialog box shows PDB files in a local PC. The user can select one or more PDB files in the FileOpen dialog box. If a single PDB file is loaded, both "Protein-RNA Interactions" and "Base Pairs" menus will be activated. If multiple PDB files are loaded, only the "Protein-RNA Interactions" menu will be activated.
The program is terminated.
Protein-RNA Interactions Menu:
If the user clicks the "Protein-RNA Interactions" menu, the "Protein-RNA Interactions" panel will appear.
Panel for analyzing Protein-RNA Interactions:
There are 20 buttons and a text box in this panel. If the user selects one of the buttons, information about the selected interaction will be displayed in the text box. If multiple PDB files are loaded, the interactions in all the PDB files are displayed. For the interactions of hydrophobic amino acids (AA), aromatic AA, aliphatic AA, polar AA, positively charged AA and negatively charged amino acids, a single PDB file can be analyzed at a time.
The "Base Pairs" menu is activated when a single PDB file is loaded. When the user selects types of base pair to be analyzed (multiple selection is possible), the selected base pairs are displayed. If the "Entire Base-Pairs" button is checked, all types of base pairs are displayed. The example below displays a G-C Watson-Crick base pair.