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 (α helix, β sheet and coil) in the whole database (46223 amino acids). The correlation coefficients are Cα=0.53, Cβ=0.51 and C_coil=0.49. By also considering the β turn state the success is 61% with Cα=0.53, Cβ=0.51, Ct=0.27 and C_coil=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