Communications of the ACM
Computer Scientists, Computational Biologists, Statisticians Designing Hiv Vaccine
The Duke Human Vaccine Institute is developing algorithms to simulate the binding of HIV antibodies such as the 2F5 antibody (blue and white) seen here bound to an HIV antigen (orange).
Credit: Duke Computer Science
Recently, the medical community has called on computer scientists, computational biologists, and statisticians to help understand why HIV researchers have been unable to help the immune system fight the virus.
The Duke Human Vaccine Institute recently recruited professor Scott Schmidler to develop algorithms that can simulate how immune system antibodies and HIV antigens bind to each other to find out why some antigens evoke antibody responses and others do not. The algorithms will allow the researchers to identify which antibodies bind to which antigens and how strongly they attach. "We've been working on algorithms for quickly sampling this high dimensional conformational space," Schmidler says.
The algorithms run on a large cluster of computers and will likely takes months to complete because of the problem's complexity, according to Schmidler. The researchers hope to use the algorithm's binding predictions to design an antigen for a vaccine that results in an antibody that neutralizes HIV.
From Scientific Computing
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Abstracts Copyright © 2011 Information Inc., Bethesda, Maryland, USA
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