AIMC Topic: Proteins

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Synergistic integration of deep learning with protein docking in cardiovascular disease treatment strategies.

IUBMB life May 15, 2024
This research delves into the exploration of the potential of tocopherol-based nanoemulsion as a therapeutic agent for cardiovascular diseases (CVD) through an in-depth molecular docking analysis. The study focuses on elucidating the molecular intera...
Molecular Docking Simulation Proteins Tocopherols Deep Learning Humans Protein Binding Cardiovascular Diseases
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Predicting hotspots for disease-causing single nucleotide variants using sequences-based coevolution, network analysis, and machine learning.

PloS one May 14, 2024
To enable personalized medicine, it is important yet highly challenging to accurately predict disease-causing mutations in target proteins at high throughput. Previous computational methods have been developed using evolutionary information in combin...
Computational Biology Evolution, Molecular Mutation Humans Algorithms Machine Learning Proteins Polymorphism, Single Nucleotide
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Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence.

Current opinion in structural biology May 13, 2024
Computational approaches can provide highly detailed insight into the molecular recognition processes that underlie drug binding, the assembly of protein complexes, and the regulation of biological functional processes. Classical simulation methods c...
Computational Biology Humans Proteins Artificial Intelligence Molecular Dynamics Simulation Models, Molecular
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A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models.

Biomolecules May 13, 2024
The quality prediction of quaternary structure models of a protein complex, in the absence of its true structure, is known as the Estimation of Model Accuracy (EMA). EMA is useful for ranking predicted protein complex structures and using them approp...
Models, Molecular Protein Structure, Quaternary Deep Learning Proteins Humans
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MISATO: machine learning dataset of protein-ligand complexes for structure-based drug discovery.

Nature computational science May 10, 2024
Large language models have greatly enhanced our ability to understand biology and chemistry, yet robust methods for structure-based drug discovery, quantum chemistry and structural biology are still sparse. Precise biomolecule-ligand interaction data...
Machine Learning Molecular Dynamics Simulation Quantum Theory Ligands Drug Discovery Proteins
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ProBAN: Neural network algorithm for predicting binding affinity in protein-protein complexes.

Proteins May 9, 2024
Determining binding affinities in protein-protein and protein-peptide complexes is a challenging task that directly impacts the development of peptide and protein pharmaceuticals. Although several models have been proposed to predict the value of the...
Protein Interaction Mapping Binding Sites Thermodynamics Algorithms Protein Binding Proteins Databases, Protein Computational Biology Neural Networks, Computer
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GNNGL-PPI: multi-category prediction of protein-protein interactions using graph neural networks based on global graphs and local subgraphs.

BMC genomics May 9, 2024
Most proteins exert their functions by interacting with other proteins, making the identification of protein-protein interactions (PPI) crucial for understanding biological activities, pathological mechanisms, and clinical therapies. Developing effec...
Protein Interaction Mapping Computational Biology Proteins Humans Algorithms Neural Networks, Computer Protein Interaction Maps
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Accurate structure prediction of biomolecular interactions with AlphaFold 3.

Nature May 8, 2024
The introduction of AlphaFold 2 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design. Here we describe our AlphaFold 3 model with a substantially...
Humans Molecular Docking Simulation Deep Learning Protein Binding Software Reproducibility of Results Ligands Nucleic Acids Antigens Antibodies Protein Conformation Proteins Ions Models, Molecular
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MolLoG: A Molecular Level Interpretability Model Bridging Local to Global for Predicting Drug Target Interactions.

Journal of chemical information and modeling May 6, 2024
Developing new pharmaceuticals is a costly and time-consuming endeavor fraught with significant safety risks. A critical aspect of drug research and disease therapy is discerning the existence of interactions between drugs and proteins. The evolution...
Proteins Drug Discovery Models, Molecular Deep Learning Pharmaceutical Preparations
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Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures.

Scientific data May 6, 2024
The advent of single-particle cryo-electron microscopy (cryo-EM) has brought forth a new era of structural biology, enabling the routine determination of large biological molecules and their complexes at atomic resolution. The high-resolution structu...
Protein Conformation Cryoelectron Microscopy Proteins Models, Molecular Artificial Intelligence
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