AIMC Topic: Protein Conformation

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Harnessing AlphaFold to reveal hERG channel conformational state secrets.

eLife Jul 14, 2025
To design safe, selective, and effective new therapies, there must be a deep understanding of the structure and function of the drug target. One of the most difficult problems to solve has been the resolution of discrete conformational states of tran...
Humans Protein Conformation ERG1 Potassium Channel Molecular Docking Simulation Molecular Dynamics Simulation
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CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches.

Journal of computer-aided molecular design Jul 13, 2025
Identifying orthosteric binding sites and predicting small molecule affinities remains a key challenge in virtual screening. While blind docking explores the entire protein surface, its precision is hindered by the vast search space. Cavity detection...
Algorithms Binding Sites Ligands Molecular Docking Simulation Machine Learning Protein Binding Protein Conformation Software Proteins
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Rprot-Vec: a deep learning approach for fast protein structure similarity calculation.

BMC bioinformatics Jul 10, 2025
BACKGROUND: Predicting protein structural similarity and detecting homologous sequences remain fundamental and challenging tasks in computational biology. Accurate identification of structural homologs enables function inference for newly discovered ...
Software Proteins Databases, Protein Deep Learning Computational Biology Protein Conformation Sequence Analysis, Protein
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Integrating Protein Language Models and Geometric Deep Learning for Peptide Toxicity Prediction.

Journal of chemical information and modeling Jul 8, 2025
Peptide toxicity prediction is a critical task in biomedical research, influencing drug safety and therapeutic development. Traditional methods, relying on sequence similarity or handcrafted features, struggle to capture the complex relationship betw...
Protein Conformation Models, Molecular Amino Acid Sequence Neural Networks, Computer Peptides Deep Learning Proteins Humans
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Harnessing protein language model for structure-based discovery of highly efficient and robust PET hydrolases.

Nature communications Jul 5, 2025
Plastic waste, particularly polyethylene terephthalate (PET), presents significant environmental challenges, driving extensive research into enzymatic biodegradation. However, existing PET hydrolases (PETases) are limited by narrow sequence diversity...
Polyethylene Terephthalates Hydrolases Molecular Dynamics Simulation Crystallography, X-Ray Protein Conformation
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Mapping the Conformational Heterogeneity Intrinsic to the Protein Native Ensemble.

Biochemistry Jul 4, 2025
In the AlphaFold era, there is a significant momentum in predicting protein structures, functionality, and mutational hotspots from deep learning approaches. In this review, we highlight how structural information is only a starting point in understa...
Protein Folding Models, Molecular Protein Conformation Humans Proteins
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Graph with Residue-Based Cross-Modal Framework Enhances Cell Function-Related Protein Properties Prediction.

Journal of chemical information and modeling Jul 3, 2025
Accurate prediction of protein properties that influence cellular functions is crucial for drug design, disease research, and guiding biological wet-lab experiments. Previous methods primarily relied on physicochemical property analysis and homologou...
Neural Networks, Computer Proteins Protein Conformation
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EquiCPI: SE(3)-Equivariant Geometric Deep Learning for Structure-Aware Prediction of Compound-Protein Interactions.

Journal of chemical information and modeling Jul 2, 2025
Accurate prediction of compound-protein interactions (CPI) remains a cornerstone challenge in computational drug discovery. While existing sequence-based approaches leverage molecular fingerprints or graph representations, they critically overlook th...
Protein Conformation Models, Molecular Ligands Proteins Deep Learning Drug Discovery Protein Binding
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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 Humans Allosteric Regulation
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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...
Protein Binding Receptors, G-Protein-Coupled Humans Allosteric Regulation Receptors, Neuropeptide Protein Conformation Molecular Dynamics Simulation Binding Sites
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