The program implements a heuristic solution to detect protein complexes from large interaction networks. More simply stating the program detects clusters (cliques) of variable density and size from graphs which are representative of protein protein interaction data of Ecoli. The Ecoli dataset is included. However the program and the heuristic is generic enough to work with any kind of complicated graphs to reveal relationships between vertices that otherwise are difficult to seperate.
The time complexity of this heuristic is N^3 as compared to N! of Brute Force Attack.
To use the program first load/read the graph (sample Ecoli graphs included) using read button (R), then display the graph using graph button (G), then run the program/heuristic using heuristic (H) button. Finally display the identified clusters/cliques using Display button (D). Using can use the Plus and Minus button to zoom in and out of the view at any time.
- What is meant by Protein-Protein Interaction
a.) Let us first define what protein is and this will lead us to protein-protein interaction. “Proteins are macromolecules. They are constructed from one or more un-branched chains of amino acids that is, they are compounds whose molecule consists of many repeated units linked together (polymers).”
b.) Proteins are the active elements of cells. They aid and control the chemical reactions that make the cell work. They receive signals from outside of the cell. They control the processes by which proteins are made from the instructions in the genes. “Hence proteins interact with other proteins to form the scaffolding that gives cells their shape and as well as parts of the linkages that stick cells together into tissues and organs”.
c.) Protein-protein interactions occur widely. These can either involve specific binding or non-specific interactions. Numerous examples of specific binding can be observed in biological systems: i. Where proteins are directed to the correct compartments of cells by binding to other proteins; ii. Protein messengers bind to protein receptors on the outer surface of cell membranes to send signals between cells; iii. Proteins form structural connections between cells; iv. Some inhibitors of enzymes are proteins; v. Proteins are modified and degraded by enzymes; vi. Interaction between different protein subunits are the basis of allosteric changes in multimers vii. Protein-protein interactions underlie very large-scale movements in organisms, such as muscle contraction.
d.) Protein-protein interactions are generally favored under conditions, which reduce the net charge on the molecules, i.e. pH values near the isoelectric point.
e.) Protein-protein association involves the specific complementary recognition of two macromolecules to form a stable assembly. Fundamental to the stabilization of protein association is the hydrophobic interaction. The term hydrophobic interaction is used to describe the gain in free energy which occurs when non-polar residues of proteins associate in an aqueous environment
Copyright 2004 released under license for research and educational use only If you want to use it commercially then permission must be sought from the developer
Asad Ali Email: asad_82 [at] yahoo.com Website: https://sites.google.com/site/asad82