Background information about the Distributed Folding Project
With the upcoming completion of the Human Genome Project, we are now capable of predicting what the amino acid sequences of different proteins in the human body will be. However, while we know the order of the amino acids, proteins do not remain in a two dimensional shapes inside the human body. They "fold" into different three dimensional shapes for various proteins and in this state are used to serve their functions inside their designated host. A protein with a distinctive amino acid chain does not simply fold is a random manner, but usually folds in a specific configuration. The force behind this phenomenon is the hydrophobic effect. This effect is due to the fact that certain parts of a protein will be attracted or repelled by water, such as long hydrocarbon chains will be repelled and groups such as hydroxy and nitrile will be attracted to the surrounding water, therefore the protien will fold as to minimize exposure by hydrocarbon chains and maximize exposure by electronegative and hydrogen bonding groups. Since the fluids that living bodies are composed of primarily consist of water, these amino acid chains fold in on themselves with the chains repelled by water tending to be part of the center of the protein to minimize the amount of their surface area exposed to the body's fluids. Those amino acid chains that are attracted to water tend to be part of the surface of the protein in order to increase the proportion of the chain expose to the body's fluids. Since the forces that act on a protein depend on what the particular amino acid sequence of a protein is, a specific protein will usually "fold" in the same manner. Due to the complexity of the forces acting upon amino acid sequences large enough to form a protein, it is extremely difficult to predict how the protein will fold, but this knowledge is vital for determining how the protein functions. Devising a way to quickly and accurately predict how a protein will fold could potentially allow researchers to devise treatments for diseases such as Alzheimer's and AIDS by introducing agents (such as enzymes or other catalysts) to modify known protien folding. The big job is finding out how protiens will fold.
By using molecular dynamics, it is possible to attempt to use the basic laws of elecrostatics and thermodynamics to simulate the folding process for a particular protein. However, such an approach is limited in its utility since it requires an enormous amount of processing power to simulate even a simple protein's folding behavior.
The Distributed Folding Project takes a different approach by utilizing a newly developed software algorithm to try to predict the conformation that a protein would be most likely to fold into. An additional piece of software analyzes the projected results and determines which of the various projected results is most likely to be correct. By utilizing a distributed computing project, it is possible to quickly create a database of billions of possible structures for a protein, and thereby obtain an accurate picture of what that folded protein would look like.
The client software, available from the official site, runs very much like the SETI@Home CLI client as a console window. The software, like SETI@Home, runs on systems running Windows, Linux, MacOSX, FreeBSD, Solaris, Irix, HP-UX, TRU64, and other operating systems, so making the project ideal for those with non-Intel hardware or non-Microsoft operating systems. Many choose to run it as a service on WindowsNT, Windows2000, or Windows XP machines. Others pair it up with add-ons like WinKDFold, which allows you to the progress and speed of processing protein structures while the program remains minimized. Information on how to download and start running the program can be found right here. We (Ars Technica Team Stir Fry) are one of the various distributed computing teams that are dedicated to running the project's client software.
Written by Aegion.