AIMC Topic: Protein Folding

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AbEpiTope-1.0: Improved antibody target prediction by use of AlphaFold and inverse folding.

Science advances Jun 13, 2025
B cell epitope prediction tools are crucial for designing vaccines and disease diagnostics. However, predicting which antigens a specific antibody binds to and their exact binding sites (epitopes) remains challenging. Here, we present AbEpiTope-1.0, ...
Computational Biology Models, Molecular Machine Learning Software Antigen-Antibody Complex Protein Folding Epitopes, B-Lymphocyte Antibodies Antigens Humans
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Reliable protein-protein docking with AlphaFold, Rosetta, and replica exchange.

eLife May 27, 2025
Despite the recent breakthrough of AlphaFold (AF) in the field of protein sequence-to-structure prediction, modeling protein interfaces and predicting protein complex structures remains challenging, especially when there is a significant conformation...
Algorithms Molecular Docking Simulation Software Proteins Protein Conformation Protein Folding Protein Binding Computational Biology
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Structural Biology in the AlphaFold Era: How Far Is Artificial Intelligence from Deciphering the Protein Folding Code?

Biomolecules May 6, 2025
Proteins are biomolecules characterized by uncommon chemical and physicochemical complexities coupled with extreme responsiveness to even minor chemical modifications or environmental variations. Since the shape that proteins assume is fundamental fo...
Protein Folding Machine Learning Computational Biology Models, Molecular Humans Proteins Protein Conformation Artificial Intelligence
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Frustration in physiology and molecular medicine.

Molecular aspects of medicine Apr 23, 2025
Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and perform chemical activities coordinating the life of cells. To perform th...
Protein Conformation Gene Regulatory Networks Protein Folding Proteins Molecular Medicine Humans Animals
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Emerging frontiers in protein structure prediction following the AlphaFold revolution.

Journal of the Royal Society, Interface Apr 16, 2025
Models of protein structures enable molecular understanding of biological processes. Current protein structure prediction tools lie at the interface of biology, chemistry and computer science. Millions of protein structure models have been generated ...
Deep Learning Computational Biology Proteins Models, Molecular Protein Conformation Protein Folding
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Unsupervised Learning of Progress Coordinates during Weighted Ensemble Simulations: Application to NTL9 Protein Folding.

Journal of chemical theory and computation Mar 19, 2025
A major challenge for many rare-event sampling strategies is the identification of progress coordinates that capture the slowest relevant motions. Machine-learning methods that can identify progress coordinates in an unsupervised manner have therefor...
Markov Chains Deep Learning Protein Folding Unsupervised Machine Learning Molecular Dynamics Simulation
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Machine learning methods to study sequence-ensemble-function relationships in disordered proteins.

Current opinion in structural biology Mar 12, 2025
Recent years have seen tremendous developments in the use of machine learning models to link amino-acid sequence, structure, and function of folded proteins. These methods are, however, rarely applicable to the wide range of proteins and sequences th...
Protein Folding Models, Molecular Amino Acid Sequence Intrinsically Disordered Proteins Protein Conformation Machine Learning Computational Biology Humans
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AI protocol for retrieving protein dynamic structures from two-dimensional infrared spectra.

Proceedings of the National Academy of Sciences of the United States of America Feb 14, 2025
Understanding the dynamic evolution of protein structures is crucial for uncovering their biological functions. Yet, real-time prediction of these dynamic structures remains a significant challenge. Two-dimensional infrared (2DIR) spectroscopy is a p...
Protein Folding Protein Conformation Machine Learning Spectrophotometry, Infrared Proteins
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Severe deviation in protein fold prediction by advanced AI: a case study.

Scientific reports Feb 8, 2025
Artificial intelligence (AI) and deep learning are making groundbreaking strides in protein structure prediction. AlphaFold is remarkable in this arena for its outstanding accuracy in modelling proteins fold based solely on their amino acid sequences...
Deep Learning Protein Conformation Proteins Computational Biology Artificial Intelligence Protein Folding Models, Molecular
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Learning the language of life with AI.

Science (New York, N.Y.) Jan 30, 2025
In 2021, a year before ChatGPT took the world by storm amid the excitement about generative artificial intelligence (AI), AlphaFold 2 cracked the 50-year-old protein-folding problem, predicting three-dimensional (3D) structures for more than 200 mill...
Proteins Artificial Intelligence Protein Folding Language
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