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Vol. 11, Issue 8, 1410-1417, August 2001

METHODS
Prediction of Protein Functional Domains from Sequences Using Artificial Neural Networks

János Murvai,¹ Kristian Vlahoviek,¹ Csaba Szepesvári,² and Sándor Pongor^1,3

¹ Protein Structure and Function Group, International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy; ² Mindmaker Ltd., Budapest 1121, Hungary

An artificial neural network (ANN) solution is described for the recognition of domains in protein sequences. A query sequence is first compared to a reference database of domain sequences by use of BLAST and the output data, encoded in the form of six parameters, are forwarded to feed-forward artificial neural networks with six input and six hidden units with sigmoidal transfer function. The recognition is based on the distribution of BLAST scores precomputed for the known domain groups in a database versus database comparison. Applications to the prediction of function are discussed.

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³ Corresponding author.

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11:1410-1417 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00

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