A drawing tool for protein interaction maps in Kohn notation

Abstract

Cancer is one of the most lethal and common diseases of today. Causes of cancer have been studied widely as it is an essential part of cancer research. Cancer is mainly caused by malfunctioning of the tumor suppressor proteins. Generally, these proteins take part in protein-protein interaction networks. Hence, to understand the suppressor proteins, it is important to study these networks. Results from this study will have great impact on the cancer research, drug design and protein engineering. For that reason, these networks are represented in network diagrams called Protein Interaction Maps to visualize and understand them better. Today, there is still a need for the standard for visualization of the protein interactions. For this reason, Kohn and his group’s MIM (Molecular Interaction Map) notation is considered to be the answer to that need. Even though there are some tools for graphical visualization of protein interactions, there is no tool that can draw protein interactions with MIM notation with full support. Thus, in this study we aimed to design a tool that can draw with Kohn’s notation. We developed MIMTool; a drawing tool for manually drawing protein interaction maps in Kohn notation. Later, as one of the most important part of our study, we added a semi-automatic map drawing feature to the tool. This feature automatically draws the interactions between physical entities using Dijkstra’s shortest path algorithm. With MIMTool, it will be much faster to draw, update and exchange molecular interaction maps. Use of this tool will save time and decrease work load.