Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning

• Published in: Methods (San Diego, Calif.) Calif.), 2016-11, Vol.110, p.97-105
• Main Authors: Du, Tianchuan, Liao, Li, Wu, Cathy H, Sun, Bilin
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence - genetics; Computational Biology - methods; Machine Learning; Protein Interaction Mapping - methods; Protein Interaction Maps - genetics; Software
• ISSN: 1046-2023; 1095-9130
• DOI: 10.1016/j.ymeth.2016.06.001

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 (specifically, stacked autoencoders) to build deep neural network models to tackled the residue-residue contact prediction problem. In tandem with interaction profile Hidden Markov Models, which was used first to extract Fisher score features from protein sequences, stacked autoencoders were deployed to extract and learn hidden abstract features. The deep learning model showed significant 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 classifiers to enhance learning, out of the Fisher score features. It is further shown that deep neural networks have significant advantages over SVM in making use of the newly extracted features.