Protein backbone angle prediction with machine learning approaches.
BACKGROUND
Protein backbone torsion angle prediction provides useful local structural information that goes beyond conventional three-state (alpha, beta and coil) secondary structure predictions. Accurate prediction of protein backbone torsion angles will substantially improve modeling procedures for local structures of protein sequence segments, especially in modeling loop conformations that do not form regular structures as in alpha-helices or beta-strands.


RESULTS
We have devised two novel automated methods in protein backbone conformational state prediction: one method is based on support vector machines (SVMs); the other method combines a standard feed-forward back-propagation artificial neural network (NN) with a local structure-based sequence profile database (LSBSP1). Extensive benchmark experiments demonstrate that both methods have improved the prediction accuracy rate over the previously published methods for conformation state prediction when using an alphabet of three or four states.


BACKGROUND
LSBSP1 and the NN algorithm have been implemented in PrISM.1, which is available from www.columbia.edu/~ay1/.


BACKGROUND
Supplementary data for the SVM method can be downloaded from the Website www.cs.columbia.edu/compbio/backbone.
Kuang
Rui
R
Department of Computer Science, Columbia University, New York, NY 10032, USA.
Leslie
Christina S
CS
Yang
An-Suei
AS
D000465:Algorithms; D000595:Amino Acid Sequence; D001185:Artificial Intelligence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016571:Neural Networks, Computer; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D013223:Statistics as Topic
D011506:Proteins