"Protein folding is a big problem, there are a large number of proteins and a lot of possible shapes/fold," explained NYU scientist Bonneau, a new faculty member at NYU's Center for Comparative Functional Genomics, with a joint appointment in Biology and Computer Sciences. "In spite of the difficulty, it is an important problem, at the heart of deciphering genomes. The shear amount of compute power needed to carry out this project makes the use of grid computing essential."
It is for this reason that scientists at NYU have teamed up with IBM. The World Community Grid (wcgrid.org) aims to create the world's largest public computing grid to undertake projects that benefit humanity. IBM has developed the technical infrastructure that serves as the grid's foundation for scientific research.
The first and second phases of the NYU research are part of the Human Proteome Folding project (HPF), which combines the power the idle cycles on millions of computers (which we call the grid) to help scientists understand how human proteins fold, the shapes they take on after folding. As computers try millions of ways to fold the chains, they attempt to fold the protein in the way it actually folds in the human body (accurately predict the structure). The best shapes/3D-structures identified for each protein are returned to the scientists for further study and public release. Knowing the shapes of proteins will help researchers understand how proteins perform their functions in vivo (in the cell) and the roles of proteins in diseases. With a greater understanding of protein structure, scientists can learn more about the biological systems that underlie most human activity (biomedical, agricultural, environments). In the end, this work is enabled by the people, around the world, who have volunteered their idle cycles by downloading the grid client (wcgrid.org).
In the first phase, NYU biologists, headed by Professor Richard Bonneau, obtained structure predictions for more than 150 genomes. For more on the Bonneau laboratory's findings, go to http://www.cs.nyu.edu/~bonneau/Struct-pred.html. In this first phase, the NYU team employed "Rosetta," a computer program used in predicting de novo protein structure--"de novo" is the modeling of proteins when there is no "real world" structure on which to base predictions.
"With the first phase we aimed to get protein function by predicting the shape of many protein structures," explained Bonneau. "With the second phase, we will increase the resolution of a select subset of human proteins (attempt to determine the structure with respect to all atoms in the molecule). This phase also include a large test set and will thus serve to improve our understanding of protein structure prediction and advance the state of the art in protein structure prediction."
The NYU researchers, working with researchers studying new methods for early detection of cancer at Seattle's Institute for Systems Biology, will focus on cancer biomarkers--proteins expressed during the early stages of several cancers. They will also focus on proteins involved in host-parasite interactions that are key to our understanding of malaria. They will use a different mode of the Rosetta program to generate higher resolution structures, thereby refining predictions from the first phase with more accurate but also much more computationally demanding methods.
James Devitt | EurekAlert!
‘Farming’ bacteria to boost growth in the oceans
24.10.2016 | Max-Planck-Institut für marine Mikrobiologie
Calcium Induces Chronic Lung Infections
24.10.2016 | Universität Basel
Terahertz excitation of selected crystal vibrations leads to an effective magnetic field that drives coherent spin motion
Controlling functional properties by light is one of the grand goals in modern condensed matter physics and materials science. A new study now demonstrates how...
Researchers from the Institute for Quantum Computing (IQC) at the University of Waterloo led the development of a new extensible wiring technique capable of controlling superconducting quantum bits, representing a significant step towards to the realization of a scalable quantum computer.
"The quantum socket is a wiring method that uses three-dimensional wires based on spring-loaded pins to address individual qubits," said Jeremy Béjanin, a PhD...
In a paper in Scientific Reports, a research team at Worcester Polytechnic Institute describes a novel light-activated phenomenon that could become the basis for applications as diverse as microscopic robotic grippers and more efficient solar cells.
A research team at Worcester Polytechnic Institute (WPI) has developed a revolutionary, light-activated semiconductor nanocomposite material that can be used...
By forcefully embedding two silicon atoms in a diamond matrix, Sandia researchers have demonstrated for the first time on a single chip all the components needed to create a quantum bridge to link quantum computers together.
"People have already built small quantum computers," says Sandia researcher Ryan Camacho. "Maybe the first useful one won't be a single giant quantum computer...
COMPAMED has become the leading international marketplace for suppliers of medical manufacturing. The trade fair, which takes place every November and is co-located to MEDICA in Dusseldorf, has been steadily growing over the past years and shows that medical technology remains a rapidly growing market.
In 2016, the joint pavilion by the IVAM Microtechnology Network, the Product Market “High-tech for Medical Devices”, will be located in Hall 8a again and will...
14.10.2016 | Event News
14.10.2016 | Event News
12.10.2016 | Event News
24.10.2016 | Earth Sciences
24.10.2016 | Life Sciences
24.10.2016 | Physics and Astronomy