Real-value prediction of backbone torsion angles.
The backbone structure of a protein is largely determined by the phi and psi torsion angles. Thus, knowing these angles, even if approximately, will be very useful for protein-structure prediction. However, in a previous work, a sequence-based, real-value prediction of psi angle could only achieve a mean absolute error of 54 degrees (83 degrees, 35 degrees, 33 degrees for coil, strand, and helix residues, respectively) between predicted and actual angles. Moreover, a real-value prediction of phi angle is not yet available. This article employs a neural-network based approach to improve psi prediction by taking advantage of angle periodicity and apply the new method to the prediction to phi angles. The 10-fold-cross-validated mean absolute error for the new method is 38 degrees (58 degrees, 33 degrees, 22 degrees for coil, strand, and helix, respectively) for psi and 25 degrees (35 degrees, 22 degrees, 16 degrees for coil, strand, and helix, respectively) for phi. The accuracy of real-value prediction is comparable to or more accurate than the predictions based on multistate classification of the phi-psi map. More accurate prediction of real-value angles will likely be useful for improving the accuracy of fold recognition and ab initio protein-structure prediction. The Real-SPINE 2.0 server is available on the website http://sparks.informatics.iupui.edu.
Xue
Bin
B
Indiana University School of Informatics, Indiana University-Purdue University, Indianapolis, Indiana 46202, USA.
Dor
Ofer
O
Faraggi
Eshel
E
Zhou
Yaoqi
Y
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry; D015203:Reproducibility of Results; D012997:Solvents; D054159:Torsion, Mechanical
D000596:Amino Acids; D011506:Proteins; D012997:Solvents