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Education

July 23, 2007: Volume 85, Number 30; Web Exclusive

Research Tools

Studying Protein Structure Can Be A Musical Experience

Linda Wang

Web Resources

Online Information For The Blind Or Visually Impaired

Independent Laboratory Access for the Blind
[http://ilab.psu.edu]
A source of information on laboratory tools and techniques being developed for blind students by Pennsylvania State University, Truman State University, and the Indiana School for the Blind & Visually Impaired
National Center for Blind Youth in Science
www.blindscience.org
A clearinghouse of science, technology, engineering, and math resources for blind youth and their parents and teachers
National Federation of the Blind
www.nfb.org
An organization of blind people working to improve the lives of blind people through advocacy, education, research, technology, and programs encouraging independence and self-confidence
American Foundation for the Blind
www.afb.org
A nonprofit organization that supports the development of tools and technology for the blind and that promotes independent and healthy living for people with vision loss
TAEVIS at Purdue University
www.taevisonline.purdue.edu
A service that provides academic tools for students who are blind, are visually impaired, or have other vision-related disabilities
gh LLC
www.ghbraille.com
An assistive technology company that helps people with visual disabilities access information, whether the source is a textbook, publication, standardized test, or website
ACS Committee on Chemists with Disabilities
membership.acs.org/c/cwd
A committee of the American Chemical Society that promotes educational and professional opportunities for individuals with disabilities who are interested in pursuing careers in chemistry and in fields requiring knowledge of chemistry

Many researchers use software such as RasMol to visualize three-dimensional structures of proteins. But what if a researcher is blind? What's the best way to navigate those same proteins?

Adam Hofer

Musical Cues Cordes demonstrates the software he developed for blind and visually impaired researchers.

Timothy Cordes, a blind medical scientist at the University of Wisconsin, Madison, faces this challenge every day in his X-ray crystallography research. In the past, he had to go through several steps to figure out the spatial relationships of atoms and amino acid residues in a protein. "For everything I wanted to look at, I'd have to go into one program and write a file and then read it in another," he says. "I realized I needed a tool to help me streamline the process."

So Cordes developed software that allows him to navigate a protein structure simply by listening through headphones for musical cues; different atoms are represented by different musical instruments. For example, if Cordes moves his cursor to a carbon atom, he might hear the sound of a piano. If he's at an oxygen atom, he might hear the sound of a flute. As he moves from one atom to another above it, the pitch increases. And if he shifts the cursor from left to right, he'll hear the sound move from his left ear to his right ear. "It's pretty intuitive," Cordes says.

He says the program can also help sighted researchers by adding another dimension to their understanding of protein structures. Cordes plans to publish a paper about his program later this year and will make the software available for free on the Internet. He says the open-source code will allow others to modify the program according to their own needs. "I'm using this tool for proteins, but three-dimensional data is all around us, and this approach could just as easily be applied to geology or architecture."

In related work published in May in Genome Biology, Rie Takahashi and Jeffrey H. Miller of the University of California, Los Angeles, converted amino acid sequences in proteins into musical notes with the goal of enabling visually impaired scientists to hear protein patterns (2007, 8, 405). Examples of their work can be found at www.mimg.ucla.edu/faculty/miller_jh/gene2music/home.html.

"By converting genomic sequences into music, we hope to achieve several goals, which include investigating sequences by the vision impaired," the authors write. "Another aim is to attract young people into molecular genetics by using the multidisciplinary approach of fusing music and science."