What are Protein Folding Software and how do they help in Research?

1. What is Protein folding?
Protein folding is simply a process in which the amino acid chain of any particular protein gets folded to get its 3D structure. The protein in its particular 3D structure becomes functionally active and the open chain format is only suitable for the process of Translation of a protein. If by any chance this protein gets opened up in chain format, it usually termed as protein denaturation which also occurs while cooking. The protein folding required several physical forces like hydrophobic and hydrophilic forces, van der Waals forces, hydrogen bonds, etc and suitable pH. It also includes several levels like primary folding, secondary folding, tertiary folding and so on.

2. How does it help scientists and researchers?
The 3D structure of any protein is very important as it defines its functions in a biological cell. When a primary amino acid chain acquired its 3D structure successfully, it gets many particular structures like epitomes, channels, binding sites and receptors that help it pursuing its functions. So, if any miss-folding happens in its structure due to any reason, it will not be able to function properly and may lead to various diseases and even syndromes. Cancer can also be considered as an outcome of a biological protein miss-folding. So, as the protein plays a vital role in the body, it becomes really very important for scientists to study protein folding. It helps in discovering treatments for various diseases, in the research of vaccines, drugs and even in identifying the cause of diseases like AIDS and Alzheimer's.

3. How does this software understand the actual proteins in plants and animals?
Such software usually works on the basis of the data already acquired through sequencing. So, it unfolds the protein, read its sequence, analyses and then interpret the results. The whole process includes many mathematical equations, algorithms, statistical data and formulas to draw any conclusions regarding any particular protein. Nothing is accurate in the field of Bioinformatics or computational biology and it just assumes the structure as per the data already available in the database.

4. How can these run on home-based computers? What are the advantages and disadvantages of the same?
Yes, there are some software that can be run at home computers and Folding@Home is one such example. Although it can be run at home, there are some specific system requirements for the same. You may require graphics processing units (GPUs), multi-core processors, etc. Such software are useful for distributes research projects where the task is distributed among the participants and they can draw the data on their home systems and then can submit it.

5. What are the benefits of this software? Can anyone work and earn from home from this software?
Many such home software is part of gaming activities including Foldit. I am not sure about actual earning from this software and yes there are reports available giving credits to the players of such games who have submitted their data for research and scientists have used that in their interpretation.

This is a very specialised areas where computer software is used to assess and find out the basic protein structure and folding to understand its final structure which is the secondary or tertiary structure along with specific folding mechanism and designs in the 3D space. The point wise answers to this query are as follows -

1. Protein is composed of amino acids. These amino acids are present in it in some three dimensional form giving the protein its characteristic shape and structure. How these are present in the protein and make a primary structure and then the protein molecules fold themselves in a particular way and shape to make the whole protein mass is known as the folding and as it is a complex process so its design of shape is assessed with the help of computer softwares and servers are used to store this data in a scientific form.

2. Protein folding mechanism and design is the basic characteristics of a protein and is very useful in drug design and understanding the chemistry behind it. This helps the scientists in the prediction of protein structure which is the key to understand its interactions with the other chemicals and human body. This is also useful in biotechnology for designing of novel enzymes. The protein chain is having places to bind with other groups of molecule and that is the way these protein react or combine with outside material so these interactions are very important to learn about the behaviour of the protein in medical context.

3. Software is only to help the scientists and researchers to assess and stimulate an equivalent design of the protein so that we can understand its structure. As the protein chain is long and complicated these computations cannot be done manually. Software is only a tool which helps us in unravelling the structure and folding of the protein in quickest time and then focus in our core research for its application and uses.

4. The programs can be run on a home computer but it would have to be used for a project where basic data should be available which can further be assimilated with the help of the software to understand the protein structure of a particular protein in the project. Program without any object and enquiry element is a void mathematical entity.

5. This software is basically for research purpose and used for generation of new data for knowing the structure of new proteins or their combinations. These are used by the persons working in bioinformatics and theoretical Chemistry. Actually there are two places where all this work is coordinated and evaluated for the benefit of the industry. One is CASP (Critical Assessment of Techniques for Protein Structure Prediction) experiment and other is the community project CAMEO3D where a continuous evaluation of protein structure prediction including the folding patterns is carried out. People interested to work in this area voluntarily can approach these two places online. The professionals working in this field might be aware of any earning potential from these works but yes these works would have value in the pharmaceutical and allied industry where practical use of the protein structure and folding is being exploited.