Protein Sequence Classification Research Articles

InterPro: the protein sequence classification resource in 2025.

InterPro (https://www.ebi.ac.uk/interpro) is a freely accessible resource for the classification of protein sequences into families. It integrates predictive models, known as signatures, from multiple member databases to classify sequences into families and predict the presence of domains and significant sites. The InterPro database provides annotations for over 200 million sequences, ensuring extensive coverage of UniProtKB, the standard repository of protein sequences, and includes mappings to several other major resources, such as Gene Ontology (GO), Protein Data Bank in Europe (PDBe) and the AlphaFold Protein Structure Database. In this publication, we report on the status of InterPro (version 101.0), detailing new developments in the database, associated web interface and software. Notable updates include the increased integration of structures predicted by AlphaFold and the enhanced description of protein families using artificial intelligence. Over the past two years, more than 5000 new InterPro entries have been created. The InterPro website now offers access to 85000 protein families and domainsfrom its member databases and serves as a long-term archive for retired databases. InterPro data, software and tools are freely available.

Elliptic geometry-based kernel matrix for improved biological sequence classification

Protein sequence classification plays a pivotal role in bioinformatics as it enables the comprehension of protein functions and their involvement in diverse biological processes. While numerous machine learning models have been proposed to tackle this challenge, traditional approaches face limitations in capturing the intricate relationships and hierarchical structures inherent in genomic sequences. These limitations stem from operating within high-dimensional non-Euclidean spaces. To address this issue, we introduce the application of the elliptic geometry-based approach for protein sequence classification. First, we transform the problem in elliptic geometry and integrate it with the Gaussian kernel to map the problem into the Mercer kernel. The Gaussian-Elliptic approach allows for the implicit mapping of data into a higher-dimensional feature space, enabling the capture of complex nonlinear relationships. This feature becomes particularly advantageous when dealing with hierarchical or tree-like structures commonly encountered in biological sequences. Experimental results highlight the effectiveness of the proposed model in protein sequence classification, showcasing the advantages of utilizing elliptic geometry in bioinformatics analyses. It outperforms state-of-the-art methods by achieving 76% and 84% accuracies for DNA and Protein datasets, respectively. Furthermore, we provide theoretical justifications for the proposed model. This study contributes to the burgeoning field of geometric deep learning, offering insights into the potential applications of elliptic representations in the analysis of biological data.

Comparison of complex-valued and real-valued neural networks for protein sequence classification

Comparison of complex-valued and real-valued neural networks for protein sequence classification

Optimizing protein sequence classification: integrating deep learning models with Bayesian optimization for enhanced biological analysis

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.

ProtienCNN‐BLSTM: An efficient deep neural network with amino acid embedding‐based model of protein sequence classification and biological analysis

ProtienCNN‐BLSTM: An efficient deep neural network with amino acid embedding‐based model of protein sequence classification and biological analysis

MoRF_ESM: Prediction of MoRFs in disordered proteins based on a deep transformer protein language model.

Molecular recognition features (MoRFs) are particular functional segments of disordered proteins, which play crucial roles in regulating the phase transition of membrane-less organelles and frequently serve as central sites in cellular interaction networks. As the association between disordered proteins and severe diseases continues to be discovered, identifying MoRFs has gained growing significance. Due to the limited number of experimentally validated MoRFs, the performance of existing MoRF's prediction algorithms is not good enough and still needs to be improved. In this research, we present a model named MoRF_ESM, which utilizes deep-learning protein representations to predict MoRFs in disordered proteins. This approach employs a pretrained ESM-2 protein language model to generate embedding representations of residues in the form of attention map matrices. These representations are combined with a self-learned TextCNN model for feature extraction and prediction. In addition, an averaging step was incorporated at the end of the MoRF_ESM model to refine the output and generate final prediction results. In comparison to other impressive methods on benchmark datasets, the MoRF_ESM approach demonstrates state-of-the-art performance, achieving [Formula: see text] higher AUC than other methods when tested on TEST1 and achieving [Formula: see text] higher AUC than other methods when tested on TEST2. These results imply that the combination of ESM-2 and TextCNN can effectively extract deep evolutionary features related to protein structure and function, along with capturing shallow pattern features located in protein sequences, and is well qualified for the prediction task of MoRFs. Given that ESM-2 is a highly versatile protein language model, the methodology proposed in this study can be readily applied to other tasks involving the classification of protein sequences.

MehNet: a vigesimal-based model by amino acid melting points generates unique ID numbers for protein sequences

The amino acid encoding plays a pivotal role in machine learning-based methods for predicting protein structure and function, as well as in protein mapping techniques. Additionally, the classification of protein sequences presents its own challenges. The current study aims to assign a constant value to each amino acid, thereby creating distinctions among protein sequences. The datasets used in this study were obtained from the UniProt Knowledgebase. Subsequently, these datasets underwent preprocessing steps, and identical sequences were categorized under the same headings. Each amino acid was ranked based on its respective melting point and was assigned a vigesimal digit. These generated vigesimal digits were subsequently converted to decimal values. The centerpiece of this methodology was the me lting point h ashi n g t able, which was given the name ‘MehNet’. Ultimately, each protein sequence was assigned a unique identification number. This approach successfully digitized protein sequences. Notably, experiments involving randomly distributed vigesimal digits for amino acids did not yield results as promising as those achieved with MehNet. The model’s classification phase, which utilizes a k-nearest neighbors (kNN) classifier, demonstrates exceptional performance in miscellaneous viral sequences. It achieves high accuracy rates, with an overall accuracy of 99.75%. Notably, it achieves an outstanding accuracy of 99.92% for the Influenza C class, highlighting its ability to distinguish closely related viral sequences. Communicated by Ramaswamy H. Sarma

NLP Based Protein Sequence Classification Through Convolutional Neural Network

NLP Based Protein Sequence Classification Through Convolutional Neural Network

PseAAC2Vec protein encoding for TCR protein sequence classification

The classification and prediction of T-cell receptors (TCRs) protein sequences are of significant interest in understanding the immune system and developing personalized immunotherapies. In this study, we propose a novel approach using Pseudo Amino Acid Composition (PseAAC) protein encoding for accurate TCR protein sequence classification. The PseAAC2Vec encoding method captures the physicochemical properties of amino acids and their local sequence information, enabling the representation of protein sequences as fixed-length feature vectors. By incorporating physicochemical properties such as hydrophobicity, polarity, charge, molecular weight, and solvent accessibility, PseAAC2Vec provides a comprehensive and informative characterization of TCR protein sequences. To evaluate the effectiveness of the proposed PseAAC2Vec encoding approach, we assembled a large dataset of TCR protein sequences with annotated classes. We applied the PseAAC2Vec encoding scheme to each sequence and generated feature vectors based on a specified window size. Subsequently, we employed state-of-the-art machine learning algorithms, such as support vector machines (SVM) and random forests (RF), to classify the TCR protein sequences. Experimental results on the benchmark dataset demonstrated the superior performance of the PseAAC2Vec-based approach compared to existing methods. The PseAAC2Vec encoding effectively captures the discriminative patterns in TCR protein sequences, leading to improved classification accuracy and robustness. Furthermore, the encoding scheme showed promising results across different window sizes, indicating its adaptability to varying sequence contexts.

Protein Sequence Classification Through Deep Learning and Encoding Strategies

Protein sequence classification is vital for understanding protein functionalities, aiding in the inference of novel protein functions. Machine learning and deep learning algorithms have revolutionized this field, offering insights into specific protein classes and functions. This study employs Natural Language Processing (NLP) techniques, including Integer and Blosum encoding, for efficient classification. SVM with count vectorizer achieves the highest accuracy of 92%, while Integer encoding with CNN surpasses NLP embedding techniques by 4%. The goal is to develop an automated system for predicting protein functionality based on sequence classification, contributing to advancements in proteomics and computational biology.

Novel tiny textural motif pattern-based RNA virus protein sequence classification model

BackgroundRNA viruses, including severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), are important human pathogens. Sequencing of the proteins produced by RNA viruses is essential for understanding disease pathogenesis and may have diagnostic and therapeutic implications. We aimed to develop an accurate and computationally efficient handcrafted feature engineering model for classifying the protein sequences of six pathogenic RNA viruses: SARS-CoV-2, influenza A, influenza B, influenza C, human respirovirus 3, and human immunodeficiency virus (HIV)-1. The first five cause primary respiratory infections; the last has some functional similarity with SARS-CoV-2, justifying the need for diagnostic differentiation. Materials and methodWe downloaded 14,787 protein sequences belonging to the six categories in FASTA format from the open-source National Center for Biotechnology Information database and transformed the sequences into numeric arrays. First, the signal was divided into overlapping blocks representing three amino acids. Tiny textural motif pattern, a new histogram-based feature extractor, was then applied to extract textural features using simple signum, lower, and upper ternary functions. 512 features were extracted for each protein sequence and fed to an iterative neighborhood component analysis function to select a study dataset-specific optimal number (34) of the most discriminative features for downstream classification using a shallow k-nearest neighbor classifier with 10-fold cross-validation.Novelties: An efficient linear time complexity is introduced for data classification, providing a robust classification approach, especially for complex datasets. Notably, this approach extends beyond the traditional binary classification focus, successfully distinguishing up to six distinct classes. Furthermore, a novel handcrafted feature extraction method is developed, significantly enhancing data analysis and yielding more precise results. ResultsThe model attained 99.71% overall 6-class classification accuracy in a data subset and 99.85% for binary classification of SARS-CoV-2 vs. HIV-1, outperforming a similar published model. ConclusionsOur simple model accurately classified the protein sequences of six pathogenic RNA viruses and can potentially be implemented in diagnostic applications to improve RNA virus disease screening.

Proto-oncogene Protein Sequence Classification using RNN and CNN with Attention Mechanism

Proto-oncogene Protein Sequence Classification using RNN and CNN with Attention Mechanism

MLapRVFL: Protein sequence prediction based on Multi-Laplacian Regularized Random Vector Functional Link

Protein sequence classification is a crucial research field in bioinformatics, playing a vital role in facilitating functional annotation, structure prediction, and gaining a deeper understanding of protein function and interactions. With the rapid development of high-throughput sequencing technologies, a vast amount of unknown protein sequence data is being generated and accumulated, leading to an increasing demand for protein classification and annotation. Existing machine learning methods still have limitations in protein sequence classification, such as low accuracy and precision of classification models, rendering them less valuable in practical applications. Additionally, these models often lack strong generalization capabilities and cannot be widely applied to various types of proteins. Therefore, accurately classifying and predicting proteins remains a challenging task. In this study, we propose a protein sequence classifier called Multi-Laplacian Regularized Random Vector Functional Link (MLapRVFL). By incorporating Multi-Laplacian and L2,1−norm regularization terms into the basic Random Vector Functional Link (RVFL) method, we effectively improve the model's generalization performance, enhance the robustness and accuracy of the classification model. The experimental results on two commonly used datasets demonstrate that MLapRVFL outperforms popular machine learning methods and achieves superior predictive performance compared to previous studies. In conclusion, the proposed MLapRVFL method makes significant contributions to protein sequence prediction.

Colorectal Cancer Classification from Protein Sequences Using Several RNN Pre-Trained Models

Bioinformatics is one field that can integrate health information with data mining applications in order to predict or analyze the patient’s information. One among the several diseases is colorectal cancer,which is horrible and rated the third leading disease in the area of cancer which leads to death in both men and women.In general, there are several intelligent methods to identify several kinds of problems in gene selection for predicting cancer,but there is no method to give a solution for patients who are diagnosed in the advanced stage.This motivated me to design theproposed approach in which we try to identify all the homo protein sequences and then train these sequences corresponding to one which causes colorectal cancer.InBioinformatics,a protein acts as one of the main agent or source to perform a biological function by interacting with molecules like Deoxyribonucleic acid (DNA), Ribonucleic acid (RNA). The function of a protein determines the healthy or diseased states of an organism. Protein interaction with other proteins can be visualized through a network called Protein-Protein Interaction Network (PPIN).In general classification of protein sequences is a very complex task. Deep learning techniques like CNN and RNN can be used to solve the problem.In computational bioinformatics,the classification of protein sequence plays an important role in determining accuracy.To improve the accuracy of our current model, the suggested method incorporates GRU, LSTM, RNN, and Customized LSTM into an RNN based architecture by optimizing the parameters in a two-way direction.Here we try to test all the models on sample protein sequences that are collected from TCGA and then determine the correctness of testing data and training data.

Predictive analysis for pathogenicity classification of H5Nx avian influenza strains using machine learning techniques.

Over the past decades, avian influenza (AI) outbreaks have been reported across different parts of the globe, resulting in large-scale economic and livestock loss and, in some cases raising concerns about their zoonotic potential. The virulence and pathogenicity of H5Nx (e.g., H5N1, H5N2) AI strains for poultry could be inferred through various approaches, and it has been frequently performed by detecting certain pathogenicity markers in their haemagglutinin (HA) gene. The utilization of predictive modeling methods represents a possible approach to exploring this genotypic-phenotypic relationship for assisting experts in determining the pathogenicity of circulating AI viruses. Therefore, the main objective of this study was to evaluate the predictive performance of different machine learning (ML) techniques for in-silico prediction of pathogenicity of H5Nx viruses in poultry, using complete genetic sequences of the HA gene. We annotated 2137 H5Nx HA gene sequences based on the presence of the polybasic HA cleavage site (HACS) with 46.33% and 53.67% of sequences previously identified as highly pathogenic (HP) and low pathogenic (LP), respectively. We compared the performance of different ML classifiers (e.g., logistic regression (LR) with the lasso and ridge regularization, random forest (RF), K-nearest neighbor (KNN), Naïve Bayes (NB), support vector machine (SVM), and convolutional neural network (CNN)) for pathogenicity classification of raw H5Nx nucleotide and protein sequences using a 10-fold cross-validation technique. We found that different ML techniques can be successfully used for the pathogenicity classification of H5 sequences with ∼99% classification accuracy. Our results indicate that for pathogenicity classification of (1) aligned deoxyribonucleic acid (DNA) and protein sequences, with NB classifier had the lowest accuracies of 98.41% (+/-0.89) and 98.31% (+/-1.06), respectively; (2) aligned DNA and protein sequences, with LR (L1/L2), KNN, SVM (radial basis function (RBF)) and CNN classifiers had the highest accuracies of 99.20% (+/-0.54) and 99.20% (+/-0.38), respectively; (3) unaligned DNA and protein sequences, with CNN's achieved accuracies of 98.54% (+/-0.68) and 99.20% (+/-0.50), respectively. ML methods show potential for regular classification of H5Nx virus pathogenicity for poultry species, particularly when sequences containing regular markers were frequently present in the training dataset.

Protein Sequence Classification Using Bidirectional Encoder Representations from Transformers (BERT) Approach

Protein Sequence Classification Using Bidirectional Encoder Representations from Transformers (BERT) Approach

GMDM: A generalized multi-dimensional distribution overlap metric for data and model quality evaluation

In this article, we design and analyze a generalized multi-dimensional distribution overlap metric (GMDM) as a generic tool for quantifying similarity or difference between two multivariate distributions for the evaluation of data and model quality. Our experiments on different real-world datasets substantiate that the proposed metric is an apposite intuitive alternative for quantification of the performance of training models and the consistency of multiple datasets. The proposed metric is suitable, for example, for image quality assessment, evaluation of unsupervised training models trained using unpaired data, image denoising models, feature embedding in protein sequence classification, and the estimation of class-specific consistency in datasets of variable dimensions such as the MNIST, ORL, and CIFAR. Furthermore, it is substantiated that the proposed metric can serve as a batch-wise consistency score to evaluate the reproducibility of the surface-enhanced Raman spectroscopy (SERS) based molecule identification model and is also applied to the domain adaptation problem in the anomaly detection task. Our results on diverse applications confirm the generalization of the proposed method and indicate a good agreement of the GMDM with conventional data quality and performance metrics.

DeepAProt: Deep learning based abiotic stress protein sequence classification and identification tool in cereals.

The impact of climate change has been alarming for the crop growth. The extreme weather conditions can stress the crops and reduce the yield of major crops belonging to Poaceae family too, that sustains 50% of the world's food calorie and 20% of protein intake. Computational approaches, such as artificial intelligence-based techniques have become the forefront of prediction-based data interpretation and plant stress responses. In this study, we proposed a novel activation function, namely, Gaussian Error Linear Unit with Sigmoid (SIELU) which was implemented in the development of a Deep Learning (DL) model along with other hyper parameters for classification of unknown abiotic stress protein sequences from crops of Poaceae family. To develop this models, data pertaining to four different abiotic stress (namely, cold, drought, heat and salinity) responsive proteins of the crops belonging to poaceae family were retrieved from public domain. It was observed that efficiency of the DL models with our proposed novel SIELU activation function outperformed the models as compared to GeLU activation function, SVM and RF with 95.11%, 80.78%, 94.97%, and 81.69% accuracy for cold, drought, heat and salinity, respectively. Also, a web-based tool, named DeepAProt (http://login1.cabgrid.res.in:5500/) was developed using flask API, along with its mobile app. This server/App will provide researchers a convenient tool, which is rapid and economical in identification of proteins for abiotic stress management in crops Poaceae family, in endeavour of higher production for food security and combating hunger, ensuring UN SDG goal 2.0.

InterPro in 2022.

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction.

A novel deep learning-assisted hybrid network for plasmodium falciparum parasite mitochondrial proteins classification.

Plasmodium falciparum is a parasitic protozoan that can cause malaria, which is a deadly disease. Therefore, the accurate identification of malaria parasite mitochondrial proteins is essential for understanding their functions and identifying novel drug targets. For classifying protein sequences, several adaptive statistical techniques have been devised. Despite significant gains, prediction performance is still constrained by the lack of appropriate feature descriptors and learning strategies in current systems. Moreover, good ground truth data is important for Artificial Intelligence (AI)-based models but there is a lack of that data in the literature. Therefore, in this work, we propose a novel hybrid network that combines 1D Convolutional Neural Network (CNN) and Bidirectional Gated Recurrent Unit (BGRU) to classify the malaria parasite mitochondrial proteins. Furthermore, we curate a sequential data that are collected from National Center for Biotechnology Information (NCBI) and UniProtKB/Swiss-Prot proteins databanks to prepare a dataset that can be used by the research community for AI-based algorithms evaluation. We obtain 4204 cases after preprocessing of the collected data and denote this set of proteins as PF4204. Finally, we conduct an ablation study on several conventional and deep models using PF4204 and the benchmark PF2095 datasets. The proposed model ‘CNN-BGRU’ obtains the accuracy values of 0.9096 and 0.9857 on PF4204 and PF2095 datasets, respectively. In addition, the CNN-BGRU is compared with state-of-the-arts, where the results illustrate that it can extract robust features and identify proteins accurately.