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...

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Bibliographic Details
Published in:Engineering reports (Hoboken, N.J.) Vol. 7; no. 2
Main Authors: Mia, Md. Mojnu, Sultana, Habiba, Amin, Md. Al, Hossain, Md. Sakhawat, Imam, Hasan, Mohiuddin, A. K. M., Mahmud, Shahin
Format: Journal Article
Language:English
Published: Hoboken, USA John Wiley & Sons, Inc 01.02.2025
Wiley
Subjects:
Accuracy
Algorithms
Amino acids
Artificial intelligence
Bioinformatics
Biomedical materials
Datasets
Design
Energy
Engineering
Machine learning
Mutagenesis
Mutation
Neural networks
NMR
Nuclear magnetic resonance
protein computational resources
protein design
protein engineering
protein engineering tools
Proteins
Research methodology
Software
Stability
ISSN:2577-8196, 2577-8196
Online Access:Get full text
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Description
Summary: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. Illustration of modern computational approaches in protein engineering, encompassing mutation analysis, protein dynamics, high‐throughput screening, and enzyme optimization to enhance de novo protein design and functional understanding
Bibliography:The authors received no specific funding for this work.
Funding
Md. Mojnu Mia and Habiba Sultana equally contributed as first author.
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ISSN:2577-8196
2577-8196
DOI:10.1002/eng2.13112