Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning.pdfVIP
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Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning.pdf
Methods 110 (2016) 97–105
Contents lists available at ScienceDirect
Methods
journal homepage: /locate/ymeth
Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning
Tianchuan Du a,?, Li Liao a,?, Cathy H. Wu a,b, Bilin Sun a
a Department of Computer and Information Sciences, University of Delaware, Newark, DE, USA b Center for Bioinformatics Computational Biology, University of Delaware, Newark, DE, USA
article info
Article history: Received 13 April 2016 Accepted 3 June 2016 Available online 6 June 2016
Keywords: Deep learning Stacked autoencoders Deep neural networks Protein-protein interaction Contact matrix Machine learning
abstract
Protein-protein interactions play essential roles in many biological processes. Acquiring knowledge of the residue-residue contact information of two interacting proteins is not only helpful in annotating functions for proteins, but also critical for structure-based drug design. The prediction of the protein residue-residue contact matrix of the interfacial regions is challenging. In this work, we introduced deep learning techniques (speci?cally, stacked autoencoders) to build deep neural network models to tackled the residue-residue contact prediction problem. In tandem with interaction pro?le Hidden Markov Models, which was used ?rst to extract Fisher score features from protein sequences, stacked autoencoders were deployed to extract and learn hidden abstract features. The deep learning model showed signi?cant improvement over the traditional machine learning model, Support Vector Machines (SVM), with the overall accuracy increased by 15% from 65.40% to 80.82%. We showed that the stacked autoencoders could extract novel features, which can be utilized by deep neural networks and other classi?ers to enhance learning, out of the Fisher score features. It is further shown that deep neural networks have signi?cant advantages over SVM in making use of the newly extracted
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