Real-SPINE: an integrated system of neural networks for real-value prediction of protein structural properties.
Proteins can move freely in three-dimensional space. As a result, their structural properties, such as solvent accessible surface area, backbone dihedral angles, and atomic distances, are continuous variables. However, these properties are often arbitrarily divided into a few classes to facilitate prediction by statistical learning techniques. In this work, we establish an integrated system of neural networks (called Real-SPINE) for real-value prediction and apply the method to predict residue-solvent accessibility and backbone psi dihedral angles of proteins based on information derived from sequences only. Real-SPINE is trained with a large data set of 2640 protein chains, sequence profiles generated from multiple sequence alignment, representative amino-acid properties, a slow learning rate, overfitting protection, and predicted secondary structures. The method optimizes more than 200,000 weights and yields a 10-fold cross-validated Pearson's correlation coefficient (PCC) of 0.74 between predicted and actual solvent accessible surface areas and 0.62 between predicted and actual psi angles. In particular, 90% of 2640 proteins have a PCC value greater than 0.6 between predicted and actual solvent-accessible surface areas. The results of Real-SPINE can be compared with the best reported correlation coefficients of 0.64-0.67 for solvent-accessible surface areas and 0.47 for psi angles. The real-SPINE server, executable programs, and datasets are freely available on http://sparks.informatics.iupui.edu.
Dor
Ofer
O
Department of Physiology and Biophysics, Howard Hughes Medical Institute Center for Single Molecule Biophysics, State University of New York at Buffalo, Buffalo, New York 14214, USA.
Zhou
Yaoqi
Y
D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D016571:Neural Networks, Computer; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D012997:Solvents / Q000737:chemistry
D011506:Proteins; D012997:Solvents