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Most of the current nonclassical proteins prediction methods involve manual feature selection, such as constructing features of samples based on the physicochemical properties of proteins and position‐specific scoring matrix (PSSM). However, these tasks require researchers to perform some tedious search work to obtain the physicochemical properties of proteins. This paper proposes an end‐to‐end nonclassical secreted protein prediction model based on deep learning, named DeepNCSPP, which employs the protein sequence information and sequence statistics information as input to predict whether it is a nonclassical secreted protein. The protein sequence information and sequence statistics information are extracted using bidirectional long‐ and short‐term memory and convolutional neural networks, respectively. Among the experiments conducted on the independent test dataset, DeepNCSPP achieved excellent results with an accuracy of 88.24%, Matthews coefficient (MCC) of 77.01%, and F1‐score of 87.50%. Independent test dataset testing and 10‐fold cross‐validation show that DeepNCSPP achieves competitive performance with state‐of‐the‐art methods and can be used as a reliable nonclassical secreted protein prediction model. A web server has been constructed for the convenience of researchers. The web link is https://www.deepncspp.top/. The source code of DeepNCSPP has been hosted on GitHub and is available online (https://github.com/xiaoliu166370/DEEPNCSPP). This paper proposes an end‐to‐end nonclassical secreted protein prediction model DeepNCSPP based on deep learning, which employs the protein sequence information and sequence statistics information as input to predict whether it is a nonclassical secreted protein. The protein sequence information and sequence statistics information are extracted using bidirectional long‐ and short‐term memory and convolutional neural networks, respectively. [ABSTRACT FROM AUTHOR]

Convolutional neural networks (CNNs) are currently among the most widely-used deep neural network (DNN) architectures available and achieve state-of-the-art performance for many problems. Originally applied to computer vision tasks, CNNs work well with any data with a spatial relationship, besides images, and have been applied to different fields. However, recent works have highlighted numerical stability challenges in DNNs, which also relates to their known sensitivity to noise injection. These challenges can jeopardise their performance and reliability. This paper investigates DeepGOPlus, a CNN that predicts protein function. DeepGOPlus has achieved state-of-the-art performance and can successfully take advantage and annotate the abounding protein sequences emerging in proteomics. We determine the numerical stability of the model's inference stage by quantifying the numerical uncertainty resulting from perturbations of the underlying floating-point data. In addition, we explore the opportunity to use reduced-precision floating point formats for DeepGOPlus inference, to reduce memory consumption and latency. This is achieved by instrumenting DeepGOPlus' execution using Monte Carlo Arithmetic, a technique that experimentally quantifies floating point operation errors and VPREC, a tool that emulates results with customizable floating point precision formats. Focus is placed on the inference stage as it is the primary deliverable of the DeepGOPlus model, widely applicable across different environments. All in all, our results show that although the DeepGOPlus CNN is very stable numerically, it can only be selectively implemented with lower-precision floating-point formats. We conclude that predictions obtained from the pre-trained DeepGOPlus model are very reliable numerically, and use existing floating-point formats efficiently. [ABSTRACT FROM AUTHOR]

Protein structure prediction is one of the main research areas in the field of Bio-informatics. The importance of proteins in drug design attracts researchers for finding the accurate tertiary structure of the protein which is dependent on its secondary structure. In this paper, we focus on improving the accuracy of protein secondary structure prediction. To do so, a Multi-scale convolutional neural network with a Gated recurrent neural network (MCNN-GRNN) is proposed. The novel amino acid encoding method along with layered convolutional neural network and Gated recurrent neural network blocks helps to retrieve local and global relationships between features, which in turn effectively classify the input protein sequence into 3 and 8 states. We have evaluated our algorithm on CullPDB, CB513, PDB25, CASP10, CASP11, CASP12, CASP13, and CASP14 datasets. We have compared our algorithm with different state-of-the-art algorithms like DCNN-SS, DCRNN, MUFOLD-SS, DLBLS_SS, and CGAN-PSSP. The Q3 accuracy of the proposed algorithm is 82–87% and Q8 accuracy is 69–77% on different datasets. [ABSTRACT FROM AUTHOR]

Efforts to enhance the accuracy of protein sequence classification are of utmost importance in driving forward biological analyses and facilitating significant medical advancements. This study presents a cutting-edge model called ProtICNN-BiLSTM, which combines attention-based Improved Convolutional Neural Networks (ICNN) and Bidirectional Long Short-Term Memory (BiLSTM) units seamlessly. Our main goal is to improve the accuracy of protein sequence classification by carefully optimizing performance through Bayesian Optimisation. ProtICNN-BiLSTM combines the power of CNN and BiLSTM architectures to effectively capture local and global protein sequence dependencies. In the proposed model, the ICNN component uses convolutional operations to identify local patterns. Captures long-range associations by analyzing sequence data forward and backwards. In advanced biological studies, Bayesian Optimisation optimizes model hyperparameters for efficiency and robustness. The model was extensively confirmed with PDB-14,189 and other protein data. We found that ProtICNN-BiLSTM outperforms traditional categorization models. Bayesian Optimization's fine-tuning and seamless integration of local and global sequence information make it effective. The precision of ProtICNN-BiLSTM improves comparative protein sequence categorization. The study improves computational bioinformatics for complex biological analysis. Good results from the ProtICNN-BiLSTM model improve protein sequence categorization. This powerful tool could improve medical and biological research. The breakthrough protein sequence classification model is ProtICNN-BiLSTM. Bayesian optimization, ICNN, and BiLSTM analyze biological data accurately. [ABSTRACT FROM AUTHOR]

Virus‒host protein‒lncRNA interaction (VHPLI) predictions are critical for decoding the molecular mechanisms of viral pathogens and host immune processes. Although VHPLI interactions have been predicted in both plants and animals, they have not been extensively studied in viruses. For the first time, we propose a new deep learning-based approach that consists mainly of a convolutional neural network and bidirectional long and short-term memory network modules in combination with transfer learning named CBIL‒VHPLI to predict viral–host protein‒lncRNA interactions. The models were first trained on large and diverse datasets (including plants, animals, etc.). Protein sequence features were extracted using a k-mer method combined with the one-hot encoding and composition–transition–distribution (CTD) methods, and lncRNA sequence features were extracted using a k-mer method combined with the one-hot encoding and Z curve methods. The results obtained on three independent external validation datasets showed that the pre-trained CBIL‒VHPLI model performed the best with an accuracy of approximately 0.9. Pretraining was followed by conducting transfer learning on a viral protein–human lncRNA dataset, and the fine-tuning results showed that the accuracy of CBIL‒VHPLI was 0.946, which was significantly greater than that of the previous models. The final case study results showed that CBIL‒VHPLI achieved a prediction reproducibility rate of 91.6% for the RIP-Seq experimental screening results. This model was then used to predict the interactions between human lncRNA PIK3CD-AS2 and the nonstructural protein 1 (NS1) of the H5N1 virus, and RNA pull-down experiments were used to prove the prediction readiness of the model in terms of prediction. The source code of CBIL‒VHPLI and the datasets used in this work are available at https://github.com/Liu-Lab-Lnu/CBIL-VHPLI for academic usage. [ABSTRACT FROM AUTHOR]

Background: Most of the important biological mechanisms and functions of transmembrane proteins (TMPs) are realized through their interactions with non-transmembrane proteins(nonTMPs). The interactions between TMPs and nonTMPs in cells play vital roles in intracellular signaling, energy metabolism, investigating membrane-crossing mechanisms, correlations between disease and drugs. Results: Despite the importance of TMP-nonTMP interactions, the study of them remains in the wet experimental stage, lacking specific and comprehensive studies in the field of bioinformatics. To fill this gap, we performed a comprehensive statistical analysis of known TMP-nonTMP interactions and constructed a deep learning-based predictor to identify potential interactions. The statistical analysis describes known TMP-nonTMP interactions from various perspectives, such as distributions of species and protein families, enrichment of GO and KEGG pathways, as well as hub proteins and subnetwork modules in the PPI network. The predictor implemented by an end-to-end deep learning model can identify potential interactions from protein primary sequence information. The experimental results over the independent validation demonstrated considerable prediction performance with an MCC of 0.541. Conclusions: To our knowledge, we were the first to focus on TMP-nonTMP interactions. We comprehensively analyzed them using bioinformatics methods and predicted them via deep learning-based solely on their sequence. This research completes a key link in the protein network, benefits the understanding of protein functions, and helps in pathogenesis studies of diseases and associated drug development. [ABSTRACT FROM AUTHOR]