Dataset Information

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking.

ABSTRACT: Homology detection enables grouping proteins into families and prediction of their structure and function. The range of application of homology-based predictions can be significantly extended by using sequence profiles and incorporation of local structural features. However, incorporation of the latter terms varies a lot between existing methods, and together with many examples of distant relations not recognized even by the best methods, suggests that further improvements are still possible.Here we describe recent improvements to the fold and function assignment system (FFAS) method, including adding optimized structural features (experimental or predicted), 'symmetrical' Z-score calculation and re-ranking the templates with a neural network. The alignment accuracy in the new FFAS-3D is now 11% higher than the original and comparable with the most accurate template-based structure prediction algorithms. At the same time, FFAS-3D has high success rate at the Structural Classification of Proteins (SCOP) family, superfamily and fold levels. Importantly, FFAS-3D results are not highly correlated with other programs suggesting that it may significantly improve meta-predictions. FFAS-3D does not require 3D structures of the templates, as using predicted features instead of structure-derived does not lead to the decrease of accuracy. Because of that, FFAS-3D can be used for databases other than Protein Data Bank (PDB) such as Protein families database or Clusters of orthologous groups thus extending its applications to functional annotations of genomes and protein families.FFAS-3D is available at http://ffas.godziklab.org.

SUBMITTER: Xu D

PROVIDER: S-EPMC3933871 | biostudies-other | 2014 Mar

REPOSITORIES: biostudies-other

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Publications

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking.

Xu Dong D Jaroszewski Lukasz L Li Zhanwen Z Godzik Adam A

Bioinformatics (Oxford, England) 20131015 5

<h4>Motivation</h4>Homology detection enables grouping proteins into families and prediction of their structure and function. The range of application of homology-based predictions can be significantly extended by using sequence profiles and incorporation of local structural features. However, incorporation of the latter terms varies a lot between existing methods, and together with many examples of distant relations not recognized even by the best methods, suggests that further improvements are ...[more]

PMID: 24130308

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Project description:Protein fold recognition is a critical step toward protein structure and function prediction, aiming at providing the most likely fold type of the query protein. In recent years, the development of deep learning (DL) technique has led to massive advances in this important field, and accordingly, the sensitivity of protein fold recognition has been dramatically improved. Most DL-based methods take an intermediate bottleneck layer as the feature representation of proteins with new fold types. However, this strategy is indirect, inefficient and conditional on the hypothesis that the bottleneck layer's representation is assumed as a good representation of proteins with new fold types. To address the above problem, in this work, we develop a new computational framework by combining triplet network and ensemble DL. We first train a DL-based model, termed FoldNet, which employs triplet loss to train the deep convolutional network. FoldNet directly optimizes the protein fold embedding itself, making the proteins with the same fold types be closer to each other than those with different fold types in the new protein embedding space. Subsequently, using the trained FoldNet, we implement a new residue-residue contact-assisted predictor, termed FoldTR, which improves protein fold recognition. Furthermore, we propose a new ensemble DL method, termed FSD_XGBoost, which combines protein fold embedding with the other two discriminative fold-specific features extracted by two DL-based methods SSAfold and DeepFR. The Top 1 sensitivity of FSD_XGBoost increases to 74.8% at the fold level, which is ~9% higher than that of the state-of-the-art method. Together, the results suggest that fold-specific features extracted by different DL methods complement with each other, and their combination can further improve fold recognition at the fold level. The implemented web server of FoldTR and benchmark datasets are publicly available at http://csbio.njust.edu.cn/bioinf/foldtr/.

Project description:Biometric technology is becoming increasingly prevalent in several vital applications that substitute traditional password and token authentication mechanisms. Recognition accuracy and computational cost are two important aspects that are to be considered while designing biometric authentication systems. Thermal imaging is proven to capture a unique thermal signature for a person and thus has been used in thermal face recognition. However, the literature did not thoroughly analyse the impact of feature selection on the accuracy and computational cost of face recognition which is an important aspect for limited resources applications like IoT ones. Also, the literature did not thoroughly evaluate the performance metrics of the proposed methods/solutions which are needed for the optimal configuration of the biometric authentication systems. This paper proposes a thermal face-based biometric authentication system. The proposed system comprises five phases: a) capturing the user's face with a thermal camera, b) segmenting the face region and excluding the background by optimized superpixel-based segmentation technique to extract the region of interest (ROI) of the face, c) feature extraction using wavelet and curvelet transform, d) feature selection by employing bio-inspired optimization algorithms: grey wolf optimizer (GWO), particle swarm optimization (PSO) and genetic algorithm (GA), e) the classification (user identification) performed using classifiers: random forest (RF), k-nearest neighbour (KNN), and naive bayes (NB). Upon the public dataset, Terravic Facial IR, the proposed system was evaluated using the metrics: accuracy, precision, recall, F-measure, and receiver operating characteristic (ROC) area. The results showed that the curvelet features optimized using the GWO and classified with random forest could help in authenticating users through thermal images with performance up to 99.5% which is better than the results of wavelet features by 10% while the former used 5% fewer features. In addition, the statistical analysis showed the significance of our proposed model. Compared to the related works, our system showed to be a better thermal face authentication model with a minimum set of features, making it computational-friendly.

Dataset Information

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking.

Publications

FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking.

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