University of Illinois researchers led by Professor John Gerlt said they are the first to use a computational method to determine the function of some of the hundreds of thousands of proteins for which amino acid sequence data are available, but whose structure and function remain unknown.

The new approach involves searching databases of known proteins for those with amino acid sequences that have the greatest homology to the unknown proteins. The researchers then use the three-dimensional structures of the most closely matched known proteins in their analyses of protein function.

Using the structural data obtained from the homology modeling, the team performs computerized docking experiments to quickly evaluate whether the unknown proteins are likely to bind to any of a vast library of potential target molecules, or substrates.

Gerlt said the finding will speed the task of identifying the biological roles of some of the hundreds of thousands of proteins whose functions have not yet been discovered.

The study appears online in the journal Nature Chemical Biology.