Identifying the interacting positions of a protein using Boolean learning and support vector machines

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It is known that in the three-dimensional structure of a protein, certain amino acids can interact with each other in order to provide structural integrity or aid in its catalytic function. If these positions are mutated the loss of this interaction usually leads to a non-functional protein. Directed evolution experiments, which probe the sequence space of a protein through mutations in search for an improved variant, frequently result in such inactive sequences. In this work, we address the use of machine learning algorithms, Boolean learning and support vector machines (SVMs), to find such pairs of amino acid positions. The recombination method of imparting mutations was simulated to create in silico sequences that were used as training data for the algorithms. The two algorithms were combined together to develop an approach that weighs the structural risk as well as the empirical risk to solve the problem. This strategy was adapted to a multi-round framework of experiments where the data generated in the present round is used to design experiments for the next round to improve the generated library, as well as the estimation of the interacting positions. It is observed that this strategy can greatly improve the number of functional variants that are generated as well as the average number of mutations that can be made in the library. (c) 2006 Published by Elsevier Ltd.
Publisher
ELSEVIER SCI LTD
Issue Date
2006-08
Language
English
Article Type
Article
Keywords

SECONDARY STRUCTURE PREDICTION; LIBRARY CONSTRUCTION; RECOMBINATION; EVOLUTION; EXAMPLES; STRATEGIES; DESIGN

Citation

COMPUTATIONAL BIOLOGY AND CHEMISTRY, v.30, no.4, pp.268 - 279

ISSN
1476-9271
DOI
10.1016/j.compbiolchem.2006.04.001
URI
http://hdl.handle.net/10203/92840
Appears in Collection
CBE-Journal Papers(저널논문)
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