Stay at home and fight the virus!

Written by Jan Philipp Wöhrle, Albert-Ludwigs-Universität Freiburg 

Dear fellows and friends of the Young Crystallographers,

We hope that you are all fit and healthy. I guess most of you are working in home office at the moment – that is perfect. Stay there! But while you are working you can help to fight the pandemic and in addition do a bit of biocrystallography using “Folding@home”.

Folding@home (FAH or F@h) is a distributed computing project for performing molecular dynamics simulations of protein dynamics. Its initial focus was on protein folding but has shifted to more biomedical problems, such as Alzheimer’s disease, cancer, COVID-19, and Ebola.” [1]

Proteins are an essential component to many biological functions and participate in virtually all processes within biological cells. They often act as enzymes, performing biochemical reactions including cell signaling, molecular transportation, and cellular regulation. As structural elements, some proteins act as a type of skeleton for cells, and as antibodies, while other proteins participate in the immune system. Before a protein can take on these roles, it must fold into a functional three-dimensional structure, a process that often occurs spontaneously and is dependent on interactions within its amino acid sequence and interactions of the amino acids with their surroundings. Protein folding is driven by the search to find the most energetically favorable conformation of the protein, i.e., its native state. Thus, understanding protein folding is critical to understanding what a protein does and how it works, and is considered a holy grail of computational biology.” [2, 3]

Visualissation of a Markov state model for proteins. Starting from a coiled state several pathways lead to differentially shaped protein states and unite to its native 2-D structure on the right.

Markov state models are used in Folding@home to model the possible shapes and folding pathways a protein can take as it condenses from its initial randomly coiled state (left) into its native 3-D structure (right). [1]

“The project uses the idle processing resources of personal computers owned by volunteers who have installed the software on their systems. Folding@home is currently based at the Washington University in St. Louis School of Medicine, under the directorship of Dr. Greg Bowman. Folding@home is one of the world’s fastest computing systems, with a speed of approximately 98.7 petaFLOPS [4] as of early March 2020, though with the influx of new users due to the coronavirus outbreak it was announced on the 20th of March that Folding@Home now has over 470 petaFLOPS of compute power, making it the world’s most powerful super computer of any kind [5]. This performance from its large-scale computing network has allowed researchers to run computationally costly atomic-level simulations of protein folding thousands of times longer than formerly achieved.” [1]

The organization is currently using its resources to combat the coronavirus pandemic and you can help to solve the problem – just follow the link: https://foldingathome.org/

If you need more information about the project visit: https://foldingathome.org/2020/03/15/coronavirus-what-were-doing-and-how-you-can-help-in-simple-terms/

Stay at home, stay healthy and – if you like – start folding ;)

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