In nature proteins are the tireless workers that keep the machinery of life in the cells up and running. The same is true in this simulator system. It is the proteins that actually do things. Currently there are several different types of proteins defined in this system, and each one has a specific function. As more and more features are added then more protein types will be added to carry out the functions necessary to perform those features.
2. Basic Protein Properties
All proteins have the basic properties shown in table 1. Each different type of protein usually has more properties defined that are specific to it. When the proteins are being loaded from the gene the first part that is loaded is the type of protein. The different protein types are discussed more in following pages. The binding ID is a tag that is used differently by each of the different types of proteins. One of the key concepts in this system is that each protein has to match up with something else in order to be able to do anything. For example, A receptor must bind a ligand in order to be active. A transcription factor must bind an enhancer in order to perform its function, and so on. The binding ID of each protein is what is used to match up a protein with its counterpart. Finally, every protein is degraded. Nothing lasts forever, and that includes the proteins in our bodies and in this simulation. At each time step a certain percentage of all of the proteins are destroyed. The degrade rate is what determines how much protein is destroyed each step.
3. Protein Types