AIMC Topic: Protein Conformation

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Machine Learning and Structural Dynamics-Based Approach to Reveal Molecular Mechanism of PTEN Missense Mutations Shared by Cancer and Autism Spectrum Disorder.

Journal of chemical information and modeling Apr 14, 2025
Missense mutations in oncogenic proteins that are concurrently associated with neurodevelopmental disorders have garnered significant attention. Phosphatase and tensin homologue (PTEN) serves as a paradigmatic model for mapping its mutational landsca...
Mutation, Missense PTEN Phosphohydrolase Neoplasms Molecular Dynamics Simulation Protein Conformation Machine Learning Autism Spectrum Disorder Humans
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DeepAssembly2: A Web Server for Protein Complex Structure Assembly Based on Domain-Domain Interactions.

Journal of molecular biology Apr 4, 2025
Proteins often perform biological functions by forming complexes, thereby accurately predicting the structure of protein complexes is crucial to understanding and mastering their functions, as well as facilitating drug discovery. Protein monomeric st...
Software Deep Learning Computational Biology Protein Domains Internet Databases, Protein Proteins Protein Conformation Models, Molecular
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Advancing Molecular Simulations: Merging Physical Models, Experiments, and AI to Tackle Multiscale Complexity.

The journal of physical chemistry letters Apr 3, 2025
Proteins and protein complexes form adaptable networks that regulate essential biochemical pathways and define cell phenotypes through dynamic mechanisms and interactions. Advances in structural biology and molecular simulations have revealed how pro...
Protein Conformation Cryoelectron Microscopy Proteins Molecular Dynamics Simulation Machine Learning
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Can Deep Learning Blind Docking Methods be Used to Predict Allosteric Compounds?

Journal of chemical information and modeling Apr 1, 2025
Allosteric compounds offer an alternative mode of inhibition to orthosteric compounds with opportunities for selectivity and noncompetition. Structure-based drug design (SBDD) of allosteric compounds introduces complications compared to their orthost...
Molecular Docking Simulation Drug Design Deep Learning Protein Kinase Inhibitors Cyclin-Dependent Kinase 2 Allosteric Regulation Ligands Protein Conformation
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Predicting protein-protein interaction with interpretable bilinear attention network.

Computer methods and programs in biomedicine Mar 30, 2025
BACKGROUND AND OBJECTIVE: Protein-protein interactions (PPIs) play the key roles in myriad biological processes, helping to understand the protein function and disease pathology. Identification of PPIs and their interaction types through wet experime...
Protein Interaction Mapping Sequence Analysis, Protein Computational Biology Proteins Algorithms Amino Acid Sequence Deep Learning Humans Databases, Protein Neural Networks, Computer Protein Conformation Protein Binding
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Fitting Atomic Structures into Cryo-EM Maps by Coupling Deep Learning-Enhanced Map Processing with Global-Local Optimization.

Journal of chemical information and modeling Mar 28, 2025
With the breakthroughs in protein structure prediction technology, constructing atomic structures from cryo-electron microscopy (cryo-EM) density maps through structural fitting has become increasingly critical. However, the accuracy of the construct...
Cryoelectron Microscopy Models, Molecular Protein Conformation Deep Learning Proteins
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Atomic context-conditioned protein sequence design using LigandMPNN.

Nature methods Mar 28, 2025
Protein sequence design in the context of small molecules, nucleotides and metals is critical to enzyme and small-molecule binder and sensor design, but current state-of-the-art deep-learning-based sequence design methods are unable to model nonprote...
Ligands Proteins Deep Learning Protein Conformation Crystallography, X-Ray Models, Molecular Protein Binding Amino Acid Sequence
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Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning.

Physical chemistry chemical physics : PCCP Mar 26, 2025
The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) are applied to explore the molecular mechanism of the ...
Protein Conformation Protein Binding Cyclin-Dependent Kinase 6 Protein Kinase Inhibitors Phosphorylation Humans Thermodynamics Molecular Dynamics Simulation Deep Learning
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TopEC: prediction of Enzyme Commission classes by 3D graph neural networks and localized 3D protein descriptor.

Nature communications Mar 20, 2025
Tools available for inferring enzyme function from general sequence, fold, or evolutionary information are generally successful. However, they can lead to misclassification if a deviation in local structural features influences the function. Here, we...
Computational Biology Protein Conformation Enzymes Graph Neural Networks Binding Sites Neural Networks, Computer Software Algorithms
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Artificial Intelligence: A New Tool for Structure-Based G Protein-Coupled Receptor Drug Discovery.

Biomolecules Mar 17, 2025
Understanding protein structures can facilitate the development of therapeutic drugs. Traditionally, protein structures have been determined through experimental approaches such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy...
Ligands Protein Conformation Drug Discovery Computational Biology Humans Receptors, G-Protein-Coupled Artificial Intelligence Algorithms Molecular Docking Simulation
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