AIMC Topic: Protein Conformation

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Modeling Active-State Conformations of G-Protein-Coupled Receptors Using AlphaFold2 via Template Bias and Explicit Protein Constrains.

Journal of chemical information and modeling May 29, 2025
AlphaFold2 and other deep learning tools represent the state of the art for protein structure prediction; however, they are still limited in their ability to model multiple protein conformations. Since the function of many proteins depends on their a...
Protein Conformation Deep Learning Models, Molecular Receptors, G-Protein-Coupled Humans Ligands
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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...
Software Algorithms Protein Conformation Computational Biology Molecular Docking Simulation Proteins Protein Folding Protein Binding
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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...
Computational Biology Proteins Models, Molecular Protein Engineering Amino Acids Protein Conformation
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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...
Protein Conformation Binding Sites Proteins Ligands Solvents Molecular Dynamics Simulation
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Cyclic peptide structure prediction and design using AlphaFold2.

Nature communications May 21, 2025
Small cyclic peptides have gained significant traction as a therapeutic modality; however, the development of deep learning methods for accurately designing such peptides has been slow, mostly due to the lack of sufficiently large training sets. Here...
Kelch-Like ECH-Associated Protein 1 Protein Conformation Proto-Oncogene Proteins c-mdm2 Peptides, Cyclic Crystallography, X-Ray Drug Design Deep Learning Humans Models, Molecular Computational Biology Amino Acid Sequence
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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...
Humans Machine Learning Computational Biology Artificial Intelligence Protein Conformation Protein Folding Proteins Models, Molecular
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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 Models, Molecular Protein Domains Proteins Databases, Protein Algorithms Deep Learning Computational Biology
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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...
History, 21st Century Computational Biology Humans Protein Conformation Proteins Artificial Intelligence Chemistry History, 20th 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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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 ...
Proteins Models, Molecular Deep Learning Protein Conformation Computational Biology Protein Folding
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