Researchers of Centrum Wiskunde & Informatica (CWI) in Amsterdam have developed a new method to compare proteins. This enables biologists to discover the function of new proteins more efficiently. The Amsterdam researchers Inken Wohlers and Gunnar Klau present their results, together with colleagues of INRIA (France), in a Featured Article in this month’s Nucleic Acid Research. The method is freely available as online application.
Biologists compare proteins to determine the function of a protein from its structure. Protein molecules consist of tens to thousands of amino acids, folded into complex, 3-dimensional shapes. This structure determines the function of the protein. Therefore, biologists compare the structure of proteins whose function is unknown to those of known proteins. Comparing proteins is also instrumental in evolutionary biology: it shows the evolutionary relationship between certain families of proteins.
Because comparing proteins accurately is difficult because of their complex structure, biologists use computer algorithms to do this. But there is no consensus over which method to use. ‘There are many criteria that can be used to compare proteins, leading to a myriad of different methods that are currently in use,’ says Wohlers. ‘We didn’t introduce new criteria, but built a general framework that incorporates existing criteria and calculates an optimal solution based on that.’
Later this year Wohlers will defend her thesis on protein structure comparison. Making biology more exact and quantitative is an important goal of the Life Sciences research at CWI.
The application can be found at http://csa.project.cwi.nl