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24 Dec 2011 04:35 AM

Improved Method For Protein Sequence Comparisons


Sequence comparisons are an essential tool for the prediction and analysis of the structure and functions of proteins. A new method developed by computational biologists at the LMU permits sequence comparisons to be performed faster and more accurately than ever before.



Lightning fast and yet highly sensitive: HHblits is a new software tool for protein research which promises to significantly improve the functional analysis of proteins. A team of computational biologists led by Dr. Johannes Söding of LMU's Genzentrum has developed a new sequence search method to identify proteins with similar sequences in databases that is faster and can discover twice as many evolutionarily related proteins as previous methods. From the functional and structural properties of the identified proteins conclusions can then be drawn on the properties of the protein to be analysed. "Our method will expand the scope and power of sequence analysis, which will in turn facilitate the experimental elucidation of the structure and function of many proteins", says Söding, who is also a member of the Center for Integrated Protein Science Munich (CiPSM). (Nature Methods, 25.12.2011).



Proteins are involved in nearly all biochemical processes of life. The functions that a protein performs largely depend on the sequence of the 20 amino acid building blocks and on the three-dimensional spatial structure into which this sequence of amino acids folds. From the similarity of protein sequences, bioinformatic methods can predict their evolutionary relatedness, which in turn implies similar structure and functions. Therefore, proteins to be studied are standardly subjected to a sequence search, in which their sequence is compared with millions of sequences in public databases with annotated structures and functions. The properties of the protein of interest can then be inferred from the properties of the proteins with similar sequences, including its structure and functions. The general relationship...
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