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 proteins 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 Bystroffs 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).
All news from this category: Life Sciences
Articles and reports from the Life Sciences 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.
Researchers confront optics and data-transfer challenges with 3D-printed lens
Researchers have developed new 3D-printed microlenses with adjustable refractive indices – a property that gives them highly specialized light-focusing abilities. This advancement is poised to improve imaging, computing and communications…
Research leads to better modeling of hypersonic flow
Hypersonic flight is conventionally referred to as the ability to fly at speeds significantly faster than the speed of sound and presents an extraordinary set of technical challenges. As an…
Researchers create ingredients to produce food by 3D printing
Food engineers in Brazil and France developed gels based on modified starch for use as “ink” to make foods and novel materials by additive manufacturing. It is already possible to…