A neural-network-based method for predicting protein stability changes upon single point mutations (original) (raw)

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Laboratory of Biocomputing, CIRB/Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy

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Laboratory of Biocomputing, CIRB/Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy

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Laboratory of Biocomputing, CIRB/Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy

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Received:

15 January 2004

Published:

04 August 2004

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Emidio Capriotti, Piero Fariselli, Rita Casadio, A neural-network-based method for predicting protein stability changes upon single point mutations, Bioinformatics, Volume 20, Issue suppl_1, August 2004, Pages i63–i68, https://doi.org/10.1093/bioinformatics/bth928
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Abstract

Motivation: One important requirement for protein design is to be able to predict changes of protein stability upon mutation. Different methods addressing this task have been described and their performance tested considering global linear correlation between predicted and experimental data. Neither is direct statistical evaluation of their prediction performance available, nor is a direct comparison among different approaches possible. Recently, a significant database of thermodynamic data on protein stability changes upon single point mutation has been generated (ProTherm). This allows the application of machine learning techniques to predicting free energy stability changes upon mutation starting from the protein sequence.

Results: In this paper, we present a neural-network-based method to predict if a given mutation increases or decreases the protein thermodynamic stability with respect to the native structure. Using a dataset consisting of 1615 mutations, our predictor correctly classifies >80% of the mutations in the database. On the same task and using the same data, our predictor performs better than other methods available on the Web. Moreover, when our system is coupled with energy-based methods, the joint prediction accuracy increases up to 90%, suggesting that it can be used to increase also the performance of pre-existing methods, and generally to improve protein design strategies.

Availability: The server is under construction and will be available at http://www.biocomp.unibo.it

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Bioinformatics 20(Suppl. 1) © Oxford University Press 2004; all rights reserved.

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