AIMC Topic: Intrinsically Disordered Proteins

Clear Filters Showing 11 to 20 of 56 articles

Accelerated Missense Mutation Identification in Intrinsically Disordered Proteins Using Deep Learning.

Biomacromolecules Mar 12, 2025
We use a combination of Brownian dynamics (BD) simulation results and deep learning (DL) strategies for the rapid identification of large structural changes caused by missense mutations in intrinsically disordered proteins (IDPs). We used ∼6500 IDP s...
Intrinsically Disordered Proteins Mutation, Missense Neural Networks, Computer Algorithms Humans Deep Learning Molecular Dynamics Simulation
View on PubMed DOI

PredIDR2: Improving accuracy of protein intrinsic disorder prediction by updating deep convolutional neural network and supplementing DisProt data.

International journal of biological macromolecules Mar 5, 2025
Intrinsically disordered proteins (IDPs) or regions (IDRs) are widespread in proteomes, and involved in several important biological processes and implicated in many diseases. Many computational methods for IDR prediction are being developed to decre...
Neural Networks, Computer Software Computational Biology Databases, Protein Intrinsically Disordered Proteins Convolutional Neural Networks ROC Curve
View on PubMed DOI

Sampling Conformational Ensembles of Highly Dynamic Proteins via Generative Deep Learning.

Journal of chemical information and modeling Feb 21, 2025
Proteins are inherently dynamic, and their conformational ensembles play a crucial role in biological function. Large-scale motions may govern the protein structure-function relationship, and numerous transient but stable conformations of intrinsical...
Deep Learning Amyloid beta-Peptides Peptide Fragments Protein Conformation Molecular Dynamics Simulation Intrinsically Disordered Proteins
View on PubMed DOI

An integrated machine learning approach delineates an entropic expansion mechanism for the binding of a small molecule to α-synuclein.

eLife Dec 18, 2024
The mis-folding and aggregation of intrinsically disordered proteins (IDPs) such as α-synuclein (αS) underlie the pathogenesis of various neurodegenerative disorders. However, targeting αS with small molecules faces challenges due to the lack of defi...
Entropy 1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine Humans Protein Conformation alpha-Synuclein Machine Learning Thermodynamics Intrinsically Disordered Proteins Protein Binding
View on PubMed DOI

PICNIC accurately predicts condensate-forming proteins regardless of their structural disorder across organisms.

Nature communications Dec 11, 2024
Biomolecular condensates are membraneless organelles that can concentrate hundreds of different proteins in cells to operate essential biological functions. However, accurate identification of their components remains challenging and biased towards p...
Proteins Amino Acid Sequence Computational Biology Proteome Intrinsically Disordered Proteins Biomolecular Condensates Humans Machine Learning Algorithms Animals
View on PubMed DOI

PredIDR: Accurate prediction of protein intrinsic disorder regions using deep convolutional neural network.

International journal of biological macromolecules Nov 19, 2024
The involvement of protein intrinsic disorder in essential biological processes, it is well known in structural biology. However, experimental methods for detecting intrinsic structural disorder and directly measuring highly dynamic behavior of prote...
Neural Networks, Computer Intrinsically Disordered Proteins Proteins Algorithms Software Computational Biology Databases, Protein
View on PubMed DOI

Emerging Frontiers in Conformational Exploration of Disordered Proteins: Integrating Autoencoder and Molecular Simulations.

ACS chemical neuroscience Nov 18, 2024
Intrinsically disordered proteins (IDPs) are closely associated with a number of neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. Due to the highly dynamic nature of IDPs, their structural determination and conformatio...
Protein Conformation Machine Learning Humans Molecular Dynamics Simulation Intrinsically Disordered Proteins
View on PubMed DOI

Deep learning for intrinsically disordered proteins: From improved predictions to deciphering conformational ensembles.

Current opinion in structural biology Nov 12, 2024
Intrinsically disordered proteins (IDPs) lack a stable three-dimensional structure under physiological conditions, challenging traditional structure-based prediction methods. This review explores how modern deep learning approaches, which have revolu...
Intrinsically Disordered Proteins Protein Conformation Deep Learning Models, Molecular Humans
View on PubMed DOI

Physics-Based Machine Learning Trains Hamiltonians and Decodes the Sequence-Conformation Relation in the Disordered Proteome.

Journal of chemical theory and computation Nov 6, 2024
Intrinsically disordered proteins and regions (IDPs) are involved in vital biological processes. To understand the IDP function, often controlled by conformation, we need to find the link between sequence and conformation. We decode this link by inte...
Machine Learning Proteome Protein Conformation Static Electricity Molecular Dynamics Simulation Intrinsically Disordered Proteins
View on PubMed DOI

Decoding Missense Variants by Incorporating Phase Separation via Machine Learning.

Nature communications Sep 27, 2024
Computational models have made significant progress in predicting the effect of protein variants. However, deciphering numerous variants of uncertain significance (VUS) located within intrinsically disordered regions (IDRs) remains challenging. To ad...
Mutation, Missense Phase Separation Computational Biology Intrinsically Disordered Proteins Humans Machine Learning
View on PubMed DOI
Popular Topics
Recent Journals