Biophysics

SPLIT PREDICTOR From amino acid sequence to secondary structure

December 1, 2004.

Lecturer

LARISA ZORANIC, M.Sc.
Faculty of Natural Sciences and Education, Split

Date and time

Monday, December 13, 2004 at 4:00 PM

Location

Lecture Hall, Wing I, Ruđer Bošković Institute, Bijenička 54, Zagreb

Abstract

How to predict the three-dimensional structure of a protein, if only the amino acid sequence is known, is one of the greatest scientific challenges of today. Information technology, i.e. bioinformatics, has developed tools that could lead to a solution to this problem. However, difficulties such as a large amount of unclassified biological data together with a small number of crystallographically known 3D structures limit bioinformatics research and emphasize the need for strict control of the obtained results. This is especially true for integral membrane proteins whose great medical and biological importance is disproportionate to the small number of known three-dimensional structures. For example, the first Croatian bioinformatics server SPLIT (http://split.pmfst.hr/split/) will describe the way of developing bioinformatics tools. The SPLIT program predicts transmembrane domains of integral membrane proteins by modeling hydrophobicity or statistical propensities of amino acid residues. The basis of the prediction is the conformational profiles calculated via propensity functions. Comparison of algorithms with already recognized bioinformatics tools showed that the SPLIT program is at the very top of the group of best predictors of transmembrane domains in the world.

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