AIMC Topic: Protein Conformation

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'Intelligent' proteins.

Cellular and molecular life sciences : CMLS Jun 14, 2025
We present an idea of protein molecules that challenges the traditional view of proteins as simple molecular machines and suggests instead that they exhibit a basic form of "intelligence". The idea stems from suggestions coming from Integrated Inform...
Proteins Protein Conformation Allosteric Regulation Humans
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Molecular insights into the unique activation and allosteric modulation mechanisms of the human mas-related G-protein-coupled receptor X1.

International journal of biological macromolecules May 30, 2025
MRGPRX1 plays dual roles in mediating nociception and pruritus, making it a promising target for alleviating itch and inhibiting pain. However, the mechanisms underlying MRGPRX1 activation and allosteric modulation remain poorly understood, posing si...
Molecular Dynamics Simulation Humans Protein Conformation Protein Binding Binding Sites Allosteric Regulation Receptors, Neuropeptide Receptors, G-Protein-Coupled
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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...
Deep Learning Models, Molecular Receptors, G-Protein-Coupled Humans Protein Conformation 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 Computational Biology Proteins Protein Conformation Molecular Docking Simulation Protein Binding Protein Folding
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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...
Protein Conformation Protein Engineering Computational Biology Models, Molecular Amino Acids 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...
Binding Sites Solvents Protein Conformation Molecular Dynamics Simulation Ligands Proteins
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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...
Humans Drug Design Crystallography, X-Ray Protein Conformation Kelch-Like ECH-Associated Protein 1 Proto-Oncogene Proteins c-mdm2 Models, Molecular Deep Learning Amino Acid Sequence Computational Biology Peptides, Cyclic
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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...
Models, Molecular Protein Conformation Protein Folding Computational Biology Proteins Artificial Intelligence Machine Learning Humans
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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...
Computational Biology Proteins Algorithms Deep Learning Protein Domains Databases, Protein Protein Conformation Models, Molecular
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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 Chemistry Protein Conformation Humans Proteins History, 20th Century Nobel Prize Artificial Intelligence
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