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Deep and self-taught learning for protein accessible surface area prediction
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Hassan, Fahad and Minhas, Fayyaz ul Amir Afsar (2017) Deep and self-taught learning for protein accessible surface area prediction. In: 2017 International Conference on Frontiers of Information Technology (FIT), Islamabad, Pakistan, 18-20 Dec 2017. Published in: 2017 International Conference on Frontiers of Information Technology (FIT) pp. 264-269. ISBN 9781538635674. doi:10.1109/FIT.2017.00054
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Official URL: https://doi.org/10.1109/FIT.2017.00054
Abstract
ASA captures the degree of burial or surface accessibility of a protein residue. It is a very important indicator of the behavior of amino acids within a protein as well. It can be used to find protein interactions, interfaces, folding states, etc. Calculation of the ASA requires the presence of the structure of the protein. However, structure determination for proteins is expensive and requires significant technical effort. As a consequence, the prediction of ASA is a very important and fundamental problem in Bioinformatics and Proteomics. In this work, we have investigated self-taught machine learning methods along with deep neural network to predict the residue level accessible surface area (ASA) of a protein. We have found that deep learning neural networks can predict the ASA of the residues in a protein accurately. Furthermore, the proposed deep learning based method does not require the use of computationally demanding features such as the position specific scoring matrix (PSSM) which have been used in previous works. A simple Blosum62 matrix based position dependent representation of amino acids in a sequence window gives comparable performance. This is particularly attractive for proteome wide prediction of ASA. We have used various self-taught learning schemes for obtaining an optimal feature representation from unlabeled data. These include a sparse and regularized autoencoder neural network and a dictionary based learning scheme. We have used unlabeled data from the protein universe in an attempt to improve the feature representation. We have also evaluated the performance of a stochastic gradient based predictor of accessible surface area for different feature representations.
| Item Type: | Conference Item (Paper) | ||||||
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| Subjects: | Q Science > QA Mathematics > QA76 Electronic computers. Computer science. Computer software Q Science > QP Physiology |
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| Divisions: | Faculty of Science > Computer Science | ||||||
| Library of Congress Subject Headings (LCSH): | Protein-protein interactions, Protein-protein interactions -- Data processing, Quadratic programming -- Computer programs, Machine learning | ||||||
| Journal or Publication Title: | 2017 International Conference on Frontiers of Information Technology (FIT) | ||||||
| Publisher: | IEEE | ||||||
| ISBN: | 9781538635674 | ||||||
| Official Date: | 18 January 2017 | ||||||
| Dates: |
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| Date of first compliant deposit: | 5 November 2019 | ||||||
| Page Range: | pp. 264-269 | ||||||
| DOI: | 10.1109/FIT.2017.00054 | ||||||
| Status: | Peer Reviewed | ||||||
| Publication Status: | Published | ||||||
| Publisher Statement: | © 2017 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. | ||||||
| Access rights to Published version: | Restricted or Subscription Access | ||||||
| Conference Paper Type: | Paper | ||||||
| Title of Event: | 2017 International Conference on Frontiers of Information Technology (FIT) | ||||||
| Type of Event: | Conference | ||||||
| Location of Event: | Islamabad, Pakistan | ||||||
| Date(s) of Event: | 18-20 Dec 2017 | ||||||
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