Application of expert networks for predicting proteins secondary structure.
The present study utilizes expert neural networks for the prediction of proteins secondary structure. We use three independent networks, one for each structure (alpha, beta and coil) as the first-level processing unit; decision upon the chosen structure for each residue is carried out by a second-level, post-processing unit, which utilizes the Chou and Fasman frequency values Falpha and Fbeta in order to strengthen and/or deplete the probability of the specific structure under investigation. The highest prediction case was 76%. Our method requires primitive computational means and a relatively small training set, while still been comparable to previous work. It is not meant to be an alternative to the determination of secondary structure by means of free energy minimization, integration of dynamic equations of motion or crystallography, which are expensive, time-consuming and complicated, but to provide additional constrains, which might be considered and incorporated into larger computing setups in order to reduce the initial search space for the above methods.
Sivan
Sarit
S
Department of Biomedical Engineering, Technion, Israel Institute of Technology, IIT, Haifa 32000, Israel. sarit@bm.technion.ac.il
Filo
Orna
O
Siegelmann
Hava
H
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D005103:Expert Systems; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D020539:Sequence Analysis, Protein / Q000379:methods*
D011506:Proteins