AIMC Topic: Proteins

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CrypToth: Cryptic Pocket Detection through Mixed-Solvent Molecular Dynamics Simulations-Based Topological Data Analysis.

Journal of chemical information and modeling May 22, 2025
Some functional proteins undergo conformational changes to expose hidden binding sites when a binding molecule approaches their surface. Such binding sites are called cryptic sites and are important targets for drug discovery. However, it is still di...
Proteins Solvents Protein Conformation Binding Sites Molecular Dynamics Simulation Ligands
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On the Difficulty to Rescore Hits from Ultralarge Docking Screens.

Journal of chemical information and modeling May 22, 2025
Docking-based virtual screening tools customized to mine ultralarge chemical spaces are consistently reported to yield both higher hit rates and more potent ligands than that achieved by conventional docking of smaller million-sized compound librarie...
Drug Evaluation, Preclinical Quantum Theory Protein Binding Machine Learning Ligands Proteins Molecular Docking Simulation
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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 Models, Molecular Protein Conformation Humans Artificial Intelligence Computational Biology Proteins Machine Learning
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M-DeepAssembly: enhanced DeepAssembly based on multi-objective multi-domain protein conformation sampling.

BMC bioinformatics May 5, 2025
BACKGROUND: Association and cooperation among structural domains play an important role in protein function and drug design. Despite remarkable advancements in highly accurate single-domain protein structure prediction through the collaborative effor...
Protein Conformation Algorithms Deep Learning Models, Molecular Protein Domains Proteins Computational Biology Databases, Protein
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Accurate identification and mechanistic evaluation of pathogenic missense variants with .

Proceedings of the National Academy of Sciences of the United States of America May 2, 2025
Understanding the effects of missense mutations or single amino acid variants (SAVs) on protein function is crucial for elucidating the molecular basis of diseases/disorders and designing rational therapies. We introduce here , a machine learning too...
Humans Mutation, Missense Algorithms Machine Learning Proteins Computational Biology Databases, Protein
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ProFun-SOM: Protein Function Prediction for Specific Ontology Based on Multiple Sequence Alignment Reconstruction.

IEEE transactions on neural networks and learning systems May 2, 2025
Protein function prediction is crucial for understanding species evolution, including viral mutations. Gene ontology (GO) is a standardized representation framework for describing protein functions with annotated terms. Each ontology is a specific fu...
Gene Ontology Sequence Alignment Databases, Protein Molecular Sequence Annotation Humans Deep Learning Computational Biology Neural Networks, Computer Proteins Algorithms
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AdptDilatedGCN: Protein-ligand binding affinity prediction based on multi-scale interaction fusion mechanism and dilated GCN.

International journal of biological macromolecules Apr 30, 2025
Predicting protein-ligand binding affinity is crucial for drug discovery. However, existing prediction methods often make insufficient use of the features of proteins and ligands, lack interactions between different information, and have difficulty i...
Ligands Deep Learning Computational Biology Protein Binding Proteins
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Massive experimental quantification allows interpretable deep learning of protein aggregation.

Science advances Apr 30, 2025
Protein aggregation is a pathological hallmark of more than 50 human diseases and a major problem for biotechnology. Methods have been proposed to predict aggregation from sequence, but these have been trained and evaluated on small and biased experi...
Proteins Protein Aggregates Deep Learning Humans Computational Biology Neural Networks, Computer
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[Nobel Prize in chemistry 2024: David Baker, Demis Hassabis et John M. Jumper. The revolution of artificial intelligence in structural biology].

Medecine sciences : M/S Apr 28, 2025
The 2024 Nobel Prize in chemistry has been awarded to Demis Hassabis and John M. Jumper (Google DeepMind) for the development of artificial intelligence-guided protein structure prediction and to David Baker (University of Washington, Seattle, USA) f...
Protein Conformation Artificial Intelligence History, 20th Century Humans Computational Biology Proteins Chemistry History, 21st Century Nobel Prize
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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...
Humans Animals Protein Conformation Protein Folding Molecular Medicine Gene Regulatory Networks Proteins
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