Intensive sequence comparisons to predict protein secondary structures. Integration into a software package: ANTHEPROT

The combination of structural class assignment with intensive sequence comparisons has permitted to develop a new concept in the prediction of the secondary structure of proteins called a self-optimised prediction method (SOPM). The accuracy of this method has been checked onto an updated release of the Kabsch & Sander database which comprises 239 protein chains. This new method correctly predicts more than 69% of amino acids for a 3-states description of the secondary structure (/spl alpha/ helix, /spl beta/ sheet and coil) in the whole database (46223 amino acids). The correlation coefficients are C/spl alpha/=0.53, C/spl beta/=0.51 and C/sub c/oil=0.49. By also considering the /spl beta/ turn state the success is 61% with C/spl alpha/=0.53, C/spl beta/=0.51, Ct=0.27 and C/sub c/oil=0.4O. RMSD as low as 10% in the secondary structure content are obtained. This method has been integrated into a software package called ANTHEPROT in order to facilitate the comparison with other methods.<
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