Prediction of secondary structure and dihedral angles in proteins

T. Zhou, N. Shu, S. Hovmoller
2008 Acta Crystallographica Section A Foundations of Crystallography  
A method for simultaneous prediction of secondary structure and dihedral angles of the polypeptide backbone in proteins is presented here. Based on a ten-fold cross-validation on a non-redundant set of 2670 protein chains with <= 25% sequence identity, the threestate accuracy (Q3) is 81-82%. Every doubling of the number of non-redundant protein chains used in the training set results in 1% better prediction of secondary structure. With the dihedral angles discretized as 8 or 3 states on the
more » ... chandran plot, the accuracies for shape symbol prediction are 68.4% and 82.1% respectively. Thus, we show here for the first time that the conformations of all amino acids in proteins can be as accurately predicted as the secondary structure. Out of the residues predicted to be random coils with accuracy of 76.5%, 69.2% of corresponding shape symbols is predicted correctly in 3-state shape classification.
doi:10.1107/s0108767308092751 fatcat:7delip4p5bcgpfxrnlpsnu2cyy