Usage
- Microsoft .NET Framework should be installed first to run PRI-Modeler.
- Input data

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.

- Menu
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.

Exit:
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.


Base Pairs Menu:
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.




Entire Base-Pairs Menu:
This example has all types of base pairs checked. When the user selects the types of base pairs and clicks the "Display H-bond base pairs" button, base pairs selected are displayed in the text window.




If the user clicks "Structure showing H-bond interactions" or "Structure showing van der Waals interactions", an RNA structure with the interactions (if any) are displayed. By moving the tick along the horizontal axis, the user can change the size of the structure drawing. The structure is visualized in the three-dimensional space, and so the user can rotate it by moving the mouse with the left mouse button pressed. The user can move the structure by moving the mouse with the right button pressed.

 

Copyright 2007 Biocomputing Lab. All rights reserved.
Biocomputing Lab, School of Computer Science and Engineering
Inha University, Inchon 402-751, Korea
phone: +82-32-860-7388, fax: +82-32-863-4386