{"title":"Significance of Sequence Features in Classification of Protein–Protein Interactions Using Machine Learning","authors":"","doi":"10.1007/s10930-023-10168-8","DOIUrl":null,"url":null,"abstract":"<h3>Abstract</h3> <p>Protein–protein interactions are crucial for the entry of viruses into the cell. Understanding the mechanism of interactions is essential in studying human-virus association, developing new biologics and drug candidates, as well as viral infections and antiviral responses. Experimental methods to analyze human-virus protein–protein interactions based on protein sequence data are time-consuming and labor-intensive, so machine learning models are being developed to predict interactions and determine large-scale interactomes between species. The present work highlights the importance of sequence features in classifying interacting and non-interacting proteins from the protein sequence data. Higher dimensional amino acid sequence features such as Amino Acid Composition (AAC), Dipeptide Composition (DPC), Grouped Amino Acid Composition (GAAC), Pseudo-Amino Acid Composition (PAAC) etc., are extracted. Following feature extraction, three datasets were created: Dataset 1 contains all of the extracted features. While Datasets 2 and 3 contain the most relevant features obtained through dimensionality reduction. To analyze the importance of high-dimensional features and their participation in protein–protein interactions, a random forest classifier is trained on three datasets. With dimensionality reduction, the model exhibited exceptional accuracy, indicating that dimensionality reduction fails to capture the complexity of interactions and the underlying relationships between human and viral proteins. As a result of retaining high-dimensional features, it is possible to capture all the characteristics of protein–protein interactions that resemble host–pathogen associations, leading to the development of biologically meaningful models. Our proposed approach is a more realistic and comprehensive classification model, leading to deeper insights and better applications in virology and drug development.</p>","PeriodicalId":793,"journal":{"name":"The Protein Journal","volume":"118 1","pages":""},"PeriodicalIF":1.9000,"publicationDate":"2023-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"The Protein Journal","FirstCategoryId":"2","ListUrlMain":"https://doi.org/10.1007/s10930-023-10168-8","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Protein–protein interactions are crucial for the entry of viruses into the cell. Understanding the mechanism of interactions is essential in studying human-virus association, developing new biologics and drug candidates, as well as viral infections and antiviral responses. Experimental methods to analyze human-virus protein–protein interactions based on protein sequence data are time-consuming and labor-intensive, so machine learning models are being developed to predict interactions and determine large-scale interactomes between species. The present work highlights the importance of sequence features in classifying interacting and non-interacting proteins from the protein sequence data. Higher dimensional amino acid sequence features such as Amino Acid Composition (AAC), Dipeptide Composition (DPC), Grouped Amino Acid Composition (GAAC), Pseudo-Amino Acid Composition (PAAC) etc., are extracted. Following feature extraction, three datasets were created: Dataset 1 contains all of the extracted features. While Datasets 2 and 3 contain the most relevant features obtained through dimensionality reduction. To analyze the importance of high-dimensional features and their participation in protein–protein interactions, a random forest classifier is trained on three datasets. With dimensionality reduction, the model exhibited exceptional accuracy, indicating that dimensionality reduction fails to capture the complexity of interactions and the underlying relationships between human and viral proteins. As a result of retaining high-dimensional features, it is possible to capture all the characteristics of protein–protein interactions that resemble host–pathogen associations, leading to the development of biologically meaningful models. Our proposed approach is a more realistic and comprehensive classification model, leading to deeper insights and better applications in virology and drug development.
期刊介绍：
The Protein Journal (formerly the Journal of Protein Chemistry) publishes original research work on all aspects of proteins and peptides. These include studies concerned with covalent or three-dimensional structure determination (X-ray, NMR, cryoEM, EPR/ESR, optical methods, etc.), computational aspects of protein structure and function, protein folding and misfolding, assembly, genetics, evolution, proteomics, molecular biology, protein engineering, protein nanotechnology, protein purification and analysis and peptide synthesis, as well as the elucidation and interpretation of the molecular bases of biological activities of proteins and peptides. We accept original research papers, reviews, mini-reviews, hypotheses, opinion papers, and letters to the editor.
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