Mapping Proteins: Researchers at Rensselaer Polytechnic Institute Discover a Better Way to Decode the Protein Language

Two researchers at Rensselaer Polytechnic Institute are creating a faster, more efficient data-mining technique to determine basic rules of how proteins form. The researchers are Mohammed Zaki, assistant professor of computer science, and Chris Bystroff, assistant professor of biology.

Researchers can identify a protein’s biological function, and therefore its specific role in disease, if they know the 3-D structure of a protein given its amino-acid sequence.

Twenty simple amino acids make up the “language” that forms the thousands of complex proteins in the human body. The idea is to discover how amino acids, or “letters,” lead to “words” or common patterns to form proteins.

With that in mind, Zaki and Bystroff’s approach involves creating a 3-D image of each known protein already recorded in the worldwide Protein Data Bank. The researchers then reduce the image to a simpler 2-D representation, called a “contact map.” The 2-D map reveals the chemical and other interactions among amino acids-data that are difficult to extract from the more complex 3-D images.

The data are mined from the contact map is then transferred into a knowledge bank of “contact rules” and used to predict unknown proteins and even how novel proteins might form.

The research is funded under a three-year, $333,928 Early Career Principal Investigator Award from the U.S. Department of Energy.

The research will appear in the IEEE (Institute of Electrical and Electronics Engineers) journal, Transactions on Systems, Man and Cybernetics in early 2003. The work will also appear in 2003 in a chapter of a book, called Handbook of Data Mining (Publisher: Lawrence Earlbaum Associates).

CONTACT: Mohammed Zaki (518) 276-6340, zaki@cs.rpi.edu
Chris Bystroff (518) 276-3185, bystrc@rpi.edu

Media Contact

Jodi Ackerman Rensselaer News and Information

All latest news from the category: Life Sciences and Chemistry

Articles and reports from the Life Sciences and chemistry area deal with applied and basic research into modern biology, chemistry and human medicine.

Valuable information can be found on a range of life sciences fields including bacteriology, biochemistry, bionics, bioinformatics, biophysics, biotechnology, genetics, geobotany, human biology, marine biology, microbiology, molecular biology, cellular biology, zoology, bioinorganic chemistry, microchemistry and environmental chemistry.

Back to home

Comments (0)

Write a comment

Newest articles

Lighting up the future

New multidisciplinary research from the University of St Andrews could lead to more efficient televisions, computer screens and lighting. Researchers at the Organic Semiconductor Centre in the School of Physics and…

Researchers crack sugarcane’s complex genetic code

Sweet success: Scientists created a highly accurate reference genome for one of the most important modern crops and found a rare example of how genes confer disease resistance in plants….

Evolution of the most powerful ocean current on Earth

The Antarctic Circumpolar Current plays an important part in global overturning circulation, the exchange of heat and CO2 between the ocean and atmosphere, and the stability of Antarctica’s ice sheets….

Partners & Sponsors