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Prediction by a neural network of outer membrane beta-strand protein topology

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1998

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Freigang, Jörg
Umhau, Stephan
Zeth, Kornelius
Breed, Jason

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Published

Erschienen in

Protein Science. 1998, 7(11), pp. 2413-2420. ISSN 0961-8368. eISSN 1469-896X. Available under: doi: 10.1002/pro.5560071119

Zusammenfassung

An artificial neural network (NN) was trained to predict the topology of bacterial outer membrane (OM) β-strand proteins. Specifically, the NN predicts the z-coordinate of Cα atoms in a coordinate frame with the outer membrane in the xy-plane, such that low z-values indicate periplasmic turns, medium z-values indicate transmembrane β-strands, and high z-values indicate extracellular loops. To obtain a training set, seven OM proteins (porins) with structures known to high resolution were aligned with their pores along the z-axis. The relationship between Cα z-values and topology was thereby established. To predict the topology of other OM proteins, all seven porins were used for the training set. Z-values (topologies) were predicted for two porins with hitherto unknown structure and for OM proteins not belonging to the porin family, all with insignificant sequence homology to the training set. The results of topology prediction compare favorably with experimental topology data.

Zusammenfassung in einer weiteren Sprache

Fachgebiet (DDC)
570 Biowissenschaften, Biologie

Schlagwörter

beta-strand prediction, cross-validation, neural network, outer membrane protein, porin, topology prediction

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ISO 690DIEDERICHS, Kay, Jörg FREIGANG, Stephan UMHAU, Kornelius ZETH, Jason BREED, 1998. Prediction by a neural network of outer membrane beta-strand protein topology. In: Protein Science. 1998, 7(11), pp. 2413-2420. ISSN 0961-8368. eISSN 1469-896X. Available under: doi: 10.1002/pro.5560071119
BibTex
@article{Diederichs1998Predi-6574,
  year={1998},
  doi={10.1002/pro.5560071119},
  title={Prediction by a neural network of outer membrane beta-strand protein topology},
  number={11},
  volume={7},
  issn={0961-8368},
  journal={Protein Science},
  pages={2413--2420},
  author={Diederichs, Kay and Freigang, Jörg and Umhau, Stephan and Zeth, Kornelius and Breed, Jason}
}
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