AIMC Topic: Protein Conformation

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Predicting the Binding of Small Molecules to Proteins through Invariant Representation of the Molecular Structure.

Journal of chemical information and modeling Aug 28, 2024
We present a computational scheme for predicting the ligands that bind to a pocket of a known structure. It is based on the generation of a general abstract representation of the molecules, which is invariant to rotations, translations, and permutati...
Machine Learning Protein Binding Proteins Small Molecule Libraries Algorithms Models, Molecular Protein Conformation Molecular Structure Binding Sites Ligands
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An end-to-end framework for the prediction of protein structure and fitness from single sequence.

Nature communications Aug 27, 2024
Significant research progress has been made in the field of protein structure and fitness prediction. Particularly, single-sequence-based structure prediction methods like ESMFold and OmegaFold achieve a balance between inference speed and prediction...
Sequence Analysis, Protein Protein Stability Protein Conformation Models, Molecular Mutation Neural Networks, Computer Computational Biology Proteins Algorithms
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Generative artificial intelligence performs rudimentary structural biology modeling.

Scientific reports Aug 21, 2024
Natural language-based generative artificial intelligence (AI) has become increasingly prevalent in scientific research. Intriguingly, capabilities of generative pre-trained transformer (GPT) language models beyond the scope of natural language tasks...
Protein Conformation Coronavirus 3C Proteases Models, Molecular Amino Acids Humans COVID-19 SARS-CoV-2 Artificial Intelligence
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Navigating the landscape of enzyme design: from molecular simulations to machine learning.

Chemical Society reviews Aug 12, 2024
Global environmental issues and sustainable development call for new technologies for fine chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the alternative to the traditional organic synthesis. However, it is c...
Animals Molecular Dynamics Simulation Biocatalysis Humans Machine Learning Substrate Specificity Protein Conformation Protein Engineering Enzymes Enzyme Activation
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CREMP: Conformer-rotamer ensembles of macrocyclic peptides for machine learning.

Scientific data Aug 9, 2024
Computational and machine learning approaches to model the conformational landscape of macrocyclic peptides have the potential to enable rational design and optimization. However, accurate, fast, and scalable methods for modeling macrocycle geometrie...
Peptides, Cyclic Protein Conformation Macrocyclic Compounds Machine Learning Peptides
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Predicting Conformational Ensembles of Intrinsically Disordered Proteins: From Molecular Dynamics to Machine Learning.

The journal of physical chemistry letters Aug 2, 2024
Intrinsically disordered proteins and regions (IDP/IDRs) are ubiquitous across all domains of life. Characterized by a lack of a stable tertiary structure, IDP/IDRs populate a diverse set of transiently formed structural states that can promiscuously...
Humans Intrinsically Disordered Proteins Molecular Dynamics Simulation Machine Learning Protein Conformation
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AI-Driven Deep Learning Techniques in Protein Structure Prediction.

International journal of molecular sciences Aug 1, 2024
Protein structure prediction is important for understanding their function and behavior. This review study presents a comprehensive review of the computational models used in predicting protein structure. It covers the progression from established pr...
Artificial Intelligence Proteins Models, Molecular Protein Conformation Deep Learning Computational Biology
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Progress in the application of artificial intelligence in molecular generation models based on protein structure.

European journal of medicinal chemistry Jul 31, 2024
The molecular generation models based on protein structures represent a cutting-edge research direction in artificial intelligence-assisted drug discovery. This article aims to comprehensively summarize the research methods and developments by analyz...
Models, Molecular Protein Conformation Drug Discovery Humans Proteins Artificial Intelligence
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Context-aware geometric deep learning for protein sequence design.

Nature communications Jul 25, 2024
Protein design and engineering are evolving at an unprecedented pace leveraging the advances in deep learning. Current models nonetheless cannot natively consider non-protein entities within the design process. Here, we introduce a deep learning appr...
Protein Engineering Amino Acid Sequence Protein Conformation Proteins Deep Learning Models, Molecular
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MDFit: automated molecular simulations workflow enables high throughput assessment of ligands-protein dynamics.

Journal of computer-aided molecular design Jul 17, 2024
Molecular dynamics (MD) simulation is a powerful tool for characterizing ligand-protein conformational dynamics and offers significant advantages over docking and other rigid structure-based computational methods. However, setting up, running, and an...
Binding Sites Ligands Protein Conformation Workflow Molecular Dynamics Simulation Humans Drug Design Machine Learning Protein Binding Proteins Software Molecular Docking Simulation
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