Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering
ABSTRACT The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de novo protein design. This review consolidates and critiques a comprehensive range of modern computational resources, offering a unique focus on...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2025-02-01
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| Series: | Engineering Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1002/eng2.13112 |
| _version_ | 1826583752574238720 |
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| author | Md. Mojnu Mia Habiba Sultana Md. Al Amin Md. Sakhawat Hossain Hasan Imam A. K. M. Mohiuddin Shahin Mahmud |
| author_facet | Md. Mojnu Mia Habiba Sultana Md. Al Amin Md. Sakhawat Hossain Hasan Imam A. K. M. Mohiuddin Shahin Mahmud |
| author_sort | Md. Mojnu Mia |
| collection | DOAJ |
| description | ABSTRACT The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de novo protein design. This review consolidates and critiques a comprehensive range of modern computational resources, offering a unique focus on their applications across diverse domains, including protein stability prediction, posttranslational modification analysis, and mutation effect evaluation. Key contributions include a detailed examination of tools integrating machine learning and artificial intelligence to enhance predictive accuracy and streamline protein engineering workflows. By highlighting underexplored tools and novel methodologies, such as advanced protein–ligand interaction predictors and neural network–based stability assessment models, this study establishes itself as a unique reference for researchers aiming to develop tailored proteins for therapeutic, industrial, and biomedical applications. |
| first_indexed | 2025-03-14T15:26:51Z |
| format | Article |
| id | doaj.art-39bf1038e52c4a5790fe2b2cdc47761b |
| institution | Directory Open Access Journal |
| issn | 2577-8196 |
| language | English |
| last_indexed | 2025-03-14T15:26:51Z |
| publishDate | 2025-02-01 |
| publisher | Wiley |
| record_format | Article |
| series | Engineering Reports |
| spelling | doaj.art-39bf1038e52c4a5790fe2b2cdc47761b2025-02-25T09:06:54ZengWileyEngineering Reports2577-81962025-02-0172n/an/a10.1002/eng2.13112Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and EngineeringMd. Mojnu Mia0Habiba Sultana1Md. Al Amin2Md. Sakhawat Hossain3Hasan Imam4A. K. M. Mohiuddin5Shahin Mahmud6Department of Biotechnology and Genetic Engineering Mawlana Bhashani Science and Technology University Santosh Tangail‐1902 BangladeshDepartment of Biotechnology and Genetic Engineering Mawlana Bhashani Science and Technology University Santosh Tangail‐1902 BangladeshDepartment of Biotechnology and Genetic Engineering Mawlana Bhashani Science and Technology University Santosh Tangail‐1902 BangladeshDepartment of Biotechnology and Genetic Engineering Mawlana Bhashani Science and Technology University Santosh Tangail‐1902 BangladeshDepartment of Biochemistry and Molecular Biology Siddheswari College Moghbazar Dhaka‐1217 BangladeshDepartment of Biotechnology and Genetic Engineering Mawlana Bhashani Science and Technology University Santosh Tangail‐1902 BangladeshDepartment of Biotechnology and Genetic Engineering Mawlana Bhashani Science and Technology University Santosh Tangail‐1902 BangladeshABSTRACT The field of protein engineering has witnessed transformative advancements, with computational tools and databases driving novel innovations in de novo protein design. This review consolidates and critiques a comprehensive range of modern computational resources, offering a unique focus on their applications across diverse domains, including protein stability prediction, posttranslational modification analysis, and mutation effect evaluation. Key contributions include a detailed examination of tools integrating machine learning and artificial intelligence to enhance predictive accuracy and streamline protein engineering workflows. By highlighting underexplored tools and novel methodologies, such as advanced protein–ligand interaction predictors and neural network–based stability assessment models, this study establishes itself as a unique reference for researchers aiming to develop tailored proteins for therapeutic, industrial, and biomedical applications.https://doi.org/10.1002/eng2.13112protein computational resourcesprotein designprotein engineeringprotein engineering tools |
| spellingShingle | Md. Mojnu Mia Habiba Sultana Md. Al Amin Md. Sakhawat Hossain Hasan Imam A. K. M. Mohiuddin Shahin Mahmud Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering Engineering Reports protein computational resources protein design protein engineering protein engineering tools |
| title | Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering |
| title_full | Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering |
| title_fullStr | Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering |
| title_full_unstemmed | Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering |
| title_short | Modern Approaches to Protein Constructions: A Comprehensive Review of Computational Tools and Databases for De Novo Protein Design and Engineering |
| title_sort | modern approaches to protein constructions a comprehensive review of computational tools and databases for de novo protein design and engineering |
| topic | protein computational resources protein design protein engineering protein engineering tools |
| url | https://doi.org/10.1002/eng2.13112 |
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