Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins.
Beta-sheet proteins have been particularly challenging for de novo structure prediction methods, which tend to pair adjacent beta-strands into beta-hairpins and produce overly local topologies. To remedy this problem and facilitate de novo prediction of beta-sheet protein structures, we have developed a neural network that classifies strand-loop-strand motifs by local hairpins and nonlocal diverging turns by using the amino acid sequence as input. The neural network is trained with a representative subset of the Protein Data Bank and achieves a prediction accuracy of 75.9 +/- 4.4% compared to a baseline prediction rate of 59.1%. Hairpins are predicted with an accuracy of 77.3 +/- 6.1%, diverging turns with an accuracy of 73.9 +/- 6.0%. Incorporation of the beta-hairpin/diverging turn classification into the ROSETTA de novo structure prediction method led to higher contact order models and somewhat improved tertiary structure predictions for a test set of 11 all-beta-proteins and 3 alphabeta-proteins. The beta-hairpin/diverging turn classification from amino acid sequences is available online for academic use (Meiler and Kuhn, 2003; www.jens-meiler.de/turnpred.html).
Kuhn
Michael
M
California Institute of Technology, Pasadena, USA.
Meiler
Jens
J
Baker
David
D
D000465:Algorithms; D020816:Amino Acid Motifs; D019295:Computational Biology; D003198:Computer Simulation; D030562:Databases, Protein; D006860:Hydrogen Bonding; D020407:Internet; D008958:Models, Molecular; D016571:Neural Networks, Computer; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012680:Sensitivity and Specificity; D012984:Software
D011506:Proteins