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BrainMaker Neural Network Software

BrainMaker Analysis of Transmembrane-spanning Protein Helices

Dr. George Dombi of Wayne State University has developed neural networks which generalize common themes found in peptides of 25 amino acid length. The sequences were sorted into two groups: transmembrane or nontransmembrance type. 1751 training examples were used. As a result of training, bacteriohodopsin was examined to determine the position of it 7 transmembrane helices.

Using several training and testing experimental procedures, test results were obtained with up to 98% accuracy. A symbolic rather than numeric representation was used. For example, the alanine position 22 was represented by the input A22 being either on or off.


INPUTS
Ala_1
Ala_2
(etc...)
Ala_25
Cys_1
Cys_2
(etc...)
Cys_25
Asp_1
Asp_2
(etc...)
Asp_25
Glu_1
Glu_2
(etc...)
Glu_25
Phe_1
Phe_2
etc...)
Phe_25
(repeated for the other 16 amino acids)

OUTPUTS
transmembrane
nontransmembrane

Reference:
Dombi, G.W. and Lawrence, J, Analysis of protein transmembrane helical regions by a neural network, Protein Science (1994) 3:557-566.