DeepConv-DTI: Prediction of drug-target interactions via deep learning with convolution on protein sequences

Identification of drug-target interactions (DTIs) plays a key role in drug discovery. The high cost and labor-intensive nature of in vitro and in vivo experiments have highlighted the importance of in silico-based DTI prediction approaches. In several computational models, conventional protein descriptors are shown to be not informative enough to predict accurate DTIs. Thus, in this study, we employ a convolutional neural network (CNN) on raw protein sequences to capture local residue patterns participating in DTIs. With CNN on protein sequences, our model performs better than previous protein descriptor-based models. In addition, our model performs better than the previous deep learning model for massive prediction of DTIs. By examining the pooled convolution results, we found that our model can detect binding sites of proteins for DTIs. In conclusion, our prediction model for detecting local residue patterns of target proteins successfully enriches the protein features of a raw protein sequence, yielding better prediction results than previous approaches.Comment: 26 pages, 7 figure

PRED-CLASS: cascading neural networks for generalized protein classification and genome-wide applications

A cascading system of hierarchical, artificial neural networks (named PRED-CLASS) is presented for the generalized classification of proteins into four distinct classes-transmembrane, fibrous, globular, and mixed-from information solely encoded in their amino acid sequences. The architecture of the individual component networks is kept very simple, reducing the number of free parameters (network synaptic weights) for faster training, improved generalization, and the avoidance of data overfitting. Capturing information from as few as 50 protein sequences spread among the four target classes (6 transmembrane, 10 fibrous, 13 globular, and 17 mixed), PRED-CLASS was able to obtain 371 correct predictions out of a set of 387 proteins (success rate approximately 96%) unambiguously assigned into one of the target classes. The application of PRED-CLASS to several test sets and complete proteomes of several organisms demonstrates that such a method could serve as a valuable tool in the annotation of genomic open reading frames with no functional assignment or as a preliminary step in fold recognition and ab initio structure prediction methods. Detailed results obtained for various data sets and completed genomes, along with a web sever running the PRED-CLASS algorithm, can be accessed over the World Wide Web at http://o2.biol.uoa.gr/PRED-CLAS

Comparison of Classifiers for Radar Emitter Type Identification

ARTMAP neural network classifiers are considered for the identification of radar emitter types from their waveform parameters. These classifiers can represent radar emitter type classes with one or more prototypes, perform on-line incremental learning to account for novelty encountered in the field, and process radar pulse streams at high speed, making them attractive for real-time applications such as electronic support measures (ESM). The performance of four ARTMAP variants- ARTMAP (Stage 1), ARTMAP-IC, fuzzy ARTMAP and Gaussian ARTMAP - is assessed with radar data gathered in the field. The k nearest neighbor (kNN) and radial basis function (RDF) classifiers are used for reference. Simulation results indicate that fuzzy ARTMAP and Gaussian ARTMAP achieve an average classification rate consistently higher than that of the other ARTMAP classifers and comparable to that of kNN and RBF. ART-EMAP, ARTMAP-IC and fuzzy ARTMAP require fewer training epochs than Gaussian ARTMAP and RBF, and substantially fewer prototype vectors (thus, smaller physical memory requirements and faster fielded performance) than Gaussian ARTMAP, RBF and kNN. Overall, fuzzy ART MAP performs at least as well as the other classifiers in both accuracy and computational complexity, and better than each of them in at least one of these aspects of performance. Incorporation into fuzzy ARTMAP of the MT- feature of ARTMAP-IC is found to be essential for convergence during on-line training with this data set.Defense Advanced Research Projects Agency and the Office of Naval Research (N000I4-95-1-409 (S.G. and M.A.R.); National Science Foundation (IRI-97-20333) (S.G.); Natural Science and Engineering Research Council of Canada (E.G.); Office of Naval Research (N00014-95-1-0657

Exploring the potential of 3D Zernike descriptors and SVM for protein\u2013protein interface prediction

Abstract Background The correct determination of protein–protein interaction interfaces is important for understanding disease mechanisms and for rational drug design. To date, several computational methods for the prediction of protein interfaces have been developed, but the interface prediction problem is still not fully understood. Experimental evidence suggests that the location of binding sites is imprinted in the protein structure, but there are major differences among the interfaces of the various protein types: the characterising properties can vary a lot depending on the interaction type and function. The selection of an optimal set of features characterising the protein interface and the development of an effective method to represent and capture the complex protein recognition patterns are of paramount importance for this task. Results In this work we investigate the potential of a novel local surface descriptor based on 3D Zernike moments for the interface prediction task. Descriptors invariant to roto-translations are extracted from circular patches of the protein surface enriched with physico-chemical properties from the HQI8 amino acid index set, and are used as samples for a binary classification problem. Support Vector Machines are used as a classifier to distinguish interface local surface patches from non-interface ones. The proposed method was validated on 16 classes of proteins extracted from the Protein–Protein Docking Benchmark 5.0 and compared to other state-of-the-art protein interface predictors (SPPIDER, PrISE and NPS-HomPPI). Conclusions The 3D Zernike descriptors are able to capture the similarity among patterns of physico-chemical and biochemical properties mapped on the protein surface arising from the various spatial arrangements of the underlying residues, and their usage can be easily extended to other sets of amino acid properties. The results suggest that the choice of a proper set of features characterising the protein interface is crucial for the interface prediction task, and that optimality strongly depends on the class of proteins whose interface we want to characterise. We postulate that different protein classes should be treated separately and that it is necessary to identify an optimal set of features for each protein class