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X-ray crystallography is the most widely used method for protein 3-dimensional structure determination. Selection of target protein that can yield high quality crystal for X-ray crystallography is a challenging task. Prediction of protein crystallization propensity from sequence information is useful for the selection of target protein for crystallization. Recently, support vector machines have been widely used to solve various biological problems. In this work, we present a SVMCRYS method which use support vector machine to classify protein sequence into 'amenable to crystallization' and 'resistant to crystallization'. SVMCRYS was trained on a dataset containing 728 sequences that gave diffraction quality crystal and 728 sequences where work had been stopped before obtaining crystal. The performance of SVMCRYS method was compared with other sequence-based crystallization prediction methods such as SECRET, CRYSTALP, OB-Score, ParCrys and XtalPred using three different datasets. SVMCRYS achieved better prediction rate with higher sensitivity and specificity. Our analysis suggests that SVMCRYS can be used to predict proteins which are amenable to crystallization and proteins which are difficult for crystallization. The SVMCRYS software, dataset and feature set can be obtained from http://www3.ntu.edu.sg/home/EPNSugan/index_files/svmcrys.htm.

Eukaryotic protein secretion generally occurs via the classical secretory pathway that traverses the ER and Golgi apparatus. Secreted proteins usually contain a signal sequence with all the essential information required to target them for secretion. However, some proteins like fibroblast growth factors (FGF-1, FGF-2), interleukins (IL-1 alpha, IL-1 beta), galectins and thioredoxin are exported by an alternative pathway. This is known as leaderless or non-classical secretion and works without a signal sequence. Most computational methods for the identification of secretory proteins use the signal peptide as indicator and are therefore not able to identify substrates of non-classical secretion. In this work, we report a random forest method, SPRED, to identify secretory proteins from protein sequences irrespective of N-terminal signal peptides, thus allowing also correct classification of non-classical secretory proteins. Training was performed on a dataset containing 600 extracellular proteins and 600 cytoplasmic and/or nuclear proteins. The algorithm was tested on 180 extracellular proteins and 1380 cytoplasmic and/or nuclear proteins. We obtained 85.92% accuracy from training and 82.18% accuracy from testing. Since SPRED does not use N-terminal signals, it can detect non-classical secreted proteins by filtering those secreted proteins with an N-terminal signal by using SignalP. SPRED predicted 15 out of 19 experimentally verified non-classical secretory proteins. By scanning the entire human proteome we identified 566 protein sequences potentially undergoing non-classical secretion. The dataset and standalone version of the SPRED software is available at http://www.inb.uni-luebeck.de/tools-demos/spred/spred., (Copyright 2009 Elsevier Inc. All rights reserved.)

Background: Odorant binding proteins (OBPs) are believed to shuttle odorants from the environment to the underlying odorant receptors, for which they could potentially serve as odorant presenters. Although several sequence based search methods have been exploited for protein family prediction, less effort has been devoted to the prediction of OBPs from sequence data and this area is more challenging due to poor sequence identity between these proteins., Results: In this paper, we propose a new algorithm that uses Regularized Least Squares Classifier (RLSC) in conjunction with multiple physicochemical properties of amino acids to predict odorant-binding proteins. The algorithm was applied to the dataset derived from Pfam and GenDiS database and we obtained overall prediction accuracy of 97.7% (94.5% and 98.4% for positive and negative classes respectively)., Conclusion: Our study suggests that RLSC is potentially useful for predicting the odorant binding proteins from sequence-derived properties irrespective of sequence similarity. Our method predicts 92.8% of 56 odorant binding proteins non-homologous to any protein in the swissprot database and 97.1% of the 414 independent dataset proteins, suggesting the usefulness of RLSC method for facilitating the prediction of odorant binding proteins from sequence information.

The organization of video information in video databases requires automatic temporal segmentation with minimal user interaction. As neural networks are capable of learning the characteristics of various video segments and clustering them accordingly, in this paper, a neural network based technique is developed to segment the video sequence into shots automatically and with a minimum number of user-defined parameters. We propose to employ growing neural gas (GNG) networks and integrate multiple frame difference features to efficiently detect shot boundaries in the video. Experimental results are presented to illustrate the good performance of the proposed scheme on real video sequences.

The widespread usage of Android-powered devices in the Internet of Things (IoT) makes them susceptible to evolving cybersecurity threats. Most healthcare devices in IoT networks, such as smart watches, smart thermometers, biosensors, and more, are powered by the Android operating system, where preserving the privacy of user-sensitive data is of utmost importance. Detecting Android malware is thus vital for protecting sensitive information and ensuring the reliability of IoT networks. This article focuses on AI-enabled Android malware detection for improving zero trust security in IoT networks, which requires Android applications to be verified and authenticated before providing access to network resources. The zero trust security model requires strict identity verification for every entity trying to access resources on a private network, regardless of whether they are inside or outside the network perimeter. Our proposed solution, DP-RFECV-FNN, an innovative approach to Android malware detection that employs Differential Privacy (DP) within a Feedforward Neural Network (FNN) designed for IoT networks under the zero trust model. By integrating DP, we ensure the confidentiality of data during the detection process, setting a new standard for privacy in cybersecurity solutions. By combining the strengths of DP and zero trust security with the powerful learning capacity of the FNN, DP-RFECV-FNN demonstrates the ability to identify both known and novel malware types and achieves higher accuracy while maintaining strict privacy controls compared with recent papers. DP-RFECV-FNN achieves an accuracy ranging from 97.78% to 99.21% while utilizing static features and 93.49% to 94.36% for dynamic features of Android applications to detect whether it is malware or benign. These results are achieved under varying privacy budgets, ranging from ϵ = 0. 1 to ϵ = 1. 0. Furthermore, our proposed feature selection pipeline enables us to outperform the state-of-the-art by significantly reducing the number of selected features and training time while improving accuracy. To the best of our knowledge, this is the first work to categorize Android malware based on both static and dynamic features through a privacy-preserving neural network model. [ABSTRACT FROM AUTHOR]