AIMC Topic: Protein Conformation

Clear Filters Showing 81 to 90 of 524 articles

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...
Coronavirus 3C Proteases COVID-19 SARS-CoV-2 Amino Acids Protein Conformation Models, Molecular Humans Artificial Intelligence
View on PubMed DOI

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...
Molecular Dynamics Simulation Biocatalysis Machine Learning Animals Humans Substrate Specificity Protein Engineering Protein Conformation Enzymes Enzyme Activation
View on PubMed DOI

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...
Machine Learning Peptides Macrocyclic Compounds Peptides, Cyclic Protein Conformation
View on PubMed DOI

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...
Machine Learning Molecular Dynamics Simulation Protein Conformation Intrinsically Disordered Proteins Humans
View on PubMed DOI

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...
Deep Learning Computational Biology Artificial Intelligence Protein Conformation Proteins Models, Molecular
View on PubMed DOI

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 Drug Discovery Protein Conformation Humans Proteins Artificial Intelligence
View on PubMed DOI

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...
Deep Learning Protein Conformation Models, Molecular Proteins Protein Engineering Amino Acid Sequence
View on PubMed DOI

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...
Ligands Protein Conformation Binding Sites Workflow Molecular Dynamics Simulation Protein Binding Proteins Software Molecular Docking Simulation Drug Design Humans Machine Learning
View on PubMed DOI

The State-of-the-Art Overview to Application of Deep Learning in Accurate Protein Design and Structure Prediction.

Topics in current chemistry (Cham) Jul 4, 2024
In recent years, there has been a notable increase in the scientific community's interest in rational protein design. The prospect of designing an amino acid sequence that can reliably fold into a desired three-dimensional structure and exhibit the i...
Algorithms Deep Learning Protein Conformation Proteins Databases, Protein
View on PubMed DOI

Accurate Prediction of Protein Structural Flexibility by Deep Learning Integrating Intricate Atomic Structures and Cryo-EM Density Information.

Nature communications Jul 2, 2024
The dynamics of proteins are crucial for understanding their mechanisms. However, computationally predicting protein dynamic information has proven challenging. Here, we propose a neural network model, RMSF-net, which outperforms previous methods and...
Protein Conformation Cryoelectron Microscopy Deep Learning Computational Biology Databases, Protein Molecular Dynamics Simulation Proteins Neural Networks, Computer
View on PubMed DOI
Popular Topics
Recent Journals