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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.
To a lesser extent, [email protected] also tries to predict a protein's final structure and determine how other molecules may interact with it, which has applications in drug design.
[email protected] is developed and operated by the Pande Laboratory at Stanford University, under the direction of Prof.
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.
Since its launch on October 1, 2000, the Pande Lab has produced 139 scientific research papers as a direct result of [email protected]
Due to the complexity of proteins' conformation or configuration space (the set of possible shapes a protein can take), and limits in computing power, all-atom molecular dynamics simulations have been severely limited in the timescales which they can study.
Despite folding occurring within a crowded cellular environment, it typically proceeds smoothly.
They can use these MSMs to reveal how proteins misfold and to quantitatively compare simulations with experiments.Unless cellular mechanisms can destroy or refold misfolded proteins, they can subsequently aggregate and cause a variety of debilitating diseases.Laboratory experiments studying these processes can be limited in scope and atomic detail, leading scientists to use physics-based computing models that, when complementing experiments, seek to provide a more complete picture of protein folding, misfolding, and aggregation.Vijay Pande, and is shared by various scientific institutions and research laboratories across the world.The project has pioneered the use of graphics processing units (GPUs), Play Station 3s, Message Passing Interface (used for computing on multi-core processors), and some Sony Xperia smartphones for distributed computing and scientific research.Protein folding is driven by the search to find the most energetically favorable conformation of the protein, i.e., its native state.