AIMC Topic: Protein Engineering

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A generalized platform for artificial intelligence-powered autonomous enzyme engineering.

Nature communications Jul 1, 2025
Proteins are the molecular machines of life with numerous applications in energy, health, and sustainability. However, engineering proteins with desired functions for practical applications remains slow, expensive, and specialist-dependent. Here we r...
Artificial Intelligence 6-Phytase Substrate Specificity Hydrogen-Ion Concentration Arabidopsis Proteins Methyltransferases Protein Engineering Yersinia Arabidopsis Machine Learning Bacterial Proteins
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Data-driven protease engineering by DNA-recording and epistasis-aware machine learning.

Nature communications Jul 1, 2025
Protein engineering has recently seen tremendous transformation due to machine learning (ML) tools that predict structure from sequence at unprecedented precision. Predicting catalytic activity, however, remains challenging, restricting our capabilit...
Machine Learning Escherichia coli Protein Engineering Peptide Hydrolases Epistasis, Genetic DNA Substrate Specificity
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Designing diverse and high-performance proteins with a large language model in the loop.

PLoS computational biology Jun 5, 2025
We present a protein engineering approach to directed evolution with machine learning that integrates a new semi-supervised neural network fitness prediction model, Seq2Fitness, and an innovative optimization algorithm, biphasic annealing for diverse...
Computational Biology Proteins Protein Engineering Mutation Machine Learning Large Language Models Neural Networks, Computer Algorithms
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EMOCPD: Efficient Attention-Based Models for Computational Protein Design Using Amino Acid Microenvironment.

Journal of chemical information and modeling May 26, 2025
Computational protein design (CPD) refers to the use of computational methods to design proteins. Traditional methods relying on energy functions and heuristic algorithms for sequence design are inefficient and do not meet the demands of the big data...
Proteins Protein Engineering Computational Biology Models, Molecular Amino Acids Protein Conformation
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Applying computational protein design to therapeutic antibody discovery - current state and perspectives.

Frontiers in immunology May 22, 2025
Machine learning applications in protein sciences have ushered in a new era for designing molecules in silico. Antibodies, which currently form the largest group of biologics in clinical use, stand to benefit greatly from this shift. Despite the prol...
Protein Engineering Computational Biology Antibodies Humans Drug Design Animals Machine Learning Drug Discovery
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Robust enzyme discovery and engineering with deep learning using CataPro.

Nature communications Mar 20, 2025
Accurate prediction of enzyme kinetic parameters is crucial for enzyme exploration and modification. Existing models face the problem of either low accuracy or poor generalization ability due to overfitting. In this work, we first developed unbiased ...
Protein Engineering Deep Learning Enzymes Kinetics
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Engineering highly active nuclease enzymes with machine learning and high-throughput screening.

Cell systems Mar 12, 2025
Optimizing enzymes to function in novel chemical environments is a central goal of synthetic biology, but optimization is often hindered by a rugged fitness landscape and costly experiments. In this work, we present TeleProt, a machine learning (ML) ...
Machine Learning High-Throughput Screening Assays Directed Molecular Evolution Protein Engineering
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Artificial Intelligence Technology Assists Enzyme Prediction and Rational Design.

Journal of agricultural and food chemistry Mar 11, 2025
Since the structure of enzymes determines their function, elucidating the structure of enzymes lays a solid foundation for deciphering their catalytic mechanism and enabling rational design. The development of artificial intelligence (AI) has sparked...
Protein Engineering Enzymes Artificial Intelligence Algorithms
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Multiplexed engineering of cytochrome P450 enzymes for promoting terpenoid synthesis in Saccharomyces cerevisiae cell factories: A review.

Biotechnology advances Mar 9, 2025
Terpenoids, also known as isoprenoids, represent the largest and most structurally diverse family of natural products, and their biosynthesis is closely related to cytochrome P450 enzymes (P450s). Given the limitations of direct extraction from natur...
Metabolic Engineering Terpenes Protein Engineering Cytochrome P-450 Enzyme System Saccharomyces cerevisiae
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Enhancing Functional Protein Design Using Heuristic Optimization and Deep Learning for Anti-Inflammatory and Gene Therapy Applications.

Proteins Feb 22, 2025
Protein sequence design is a highly challenging task, aimed at discovering new proteins that are more functional and producible under laboratory conditions than their natural counterparts. Deep learning-based approaches developed to address this prob...
Anti-Inflammatory Agents Amino Acid Sequence Proteins Models, Molecular Genetic Therapy Protein Engineering Heuristics Protein Conformation Humans Algorithms Deep Learning
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