AIMC Topic: Protein Conformation

Clear Filters Showing 91 to 100 of 609 articles

Toward deep learning sequence-structure co-generation for protein design.

Current opinion in structural biology Feb 20, 2025
Deep generative models that learn from the distribution of natural protein sequences and structures may enable the design of new proteins with valuable functions. While the majority of today's models focus on generating either sequences or structures...
Protein Engineering Deep Learning Models, Molecular Proteins Protein Conformation
View on PubMed DOI

Dynamic Electronic Structure Fluctuations in the De Novo Peptide ACC-Dimer Revealed by First-Principles Theory and Machine Learning.

Journal of chemical information and modeling Feb 14, 2025
Recent studies have reported long-range charge transport in peptide- and protein-based fibers and wires, rendering this class of materials as promising charge-conducting interfaces between biological systems and electronic devices. In the complex mol...
Protein Conformation Protein Multimerization Molecular Dynamics Simulation Electrons Machine Learning Peptides Density Functional Theory
View on PubMed DOI

AI protocol for retrieving protein dynamic structures from two-dimensional infrared spectra.

Proceedings of the National Academy of Sciences of the United States of America Feb 14, 2025
Understanding the dynamic evolution of protein structures is crucial for uncovering their biological functions. Yet, real-time prediction of these dynamic structures remains a significant challenge. Two-dimensional infrared (2DIR) spectroscopy is a p...
Spectrophotometry, Infrared Machine Learning Proteins Protein Folding Protein Conformation
View on PubMed DOI

Simpler Protein Domain Identification Using Spectral Clustering.

Proteins Feb 13, 2025
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spect...
Computational Biology Cluster Analysis Proteins Algorithms Deep Learning Protein Conformation Sequence Alignment Sequence Analysis, Protein Protein Domains Databases, Protein Amino Acid Sequence Models, Molecular
View on PubMed DOI

Identification and understanding of allostery hotspots in proteins: Integration of deep mutational scanning and multi-faceted computational analyses.

Journal of molecular biology Feb 12, 2025
Motivated by recent deep mutational scanning (DMS) experiments, we have carried out a diverse set of computations to better understand the distribution and contributions of allostery hotspot residues in a transcription factor, TetR. These include ext...
Models, Molecular Mutation Computational Biology Proteins Thermodynamics Allosteric Site Molecular Dynamics Simulation Allosteric Regulation Protein Conformation Machine Learning Protein Binding
View on PubMed DOI

Modeling Boltzmann-weighted structural ensembles of proteins using artificial intelligence-based methods.

Current opinion in structural biology Feb 8, 2025
This review highlights recent advances in AI-driven methods for generating Boltzmann-weighted structural ensembles, which are crucial for understanding biomolecular dynamics and drug discovery. With the rise of deep learning models such as AlphaFold2...
Models, Molecular Molecular Dynamics Simulation Protein Conformation Deep Learning Proteins Artificial Intelligence Drug Discovery
View on PubMed DOI

Severe deviation in protein fold prediction by advanced AI: a case study.

Scientific reports Feb 8, 2025
Artificial intelligence (AI) and deep learning are making groundbreaking strides in protein structure prediction. AlphaFold is remarkable in this arena for its outstanding accuracy in modelling proteins fold based solely on their amino acid sequences...
Protein Folding Models, Molecular Protein Conformation Computational Biology Proteins Artificial Intelligence Deep Learning
View on PubMed DOI

Advancing structure modeling from cryo-EM maps with deep learning.

Biochemical Society transactions Feb 7, 2025
Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling the determination of biomolecular structures that are challenging to resolve using conventional methods. Interpreting a cryo-EM map requires accurate modeling of the...
Deep Learning Proteins Protein Conformation Cryoelectron Microscopy Models, Molecular
View on PubMed DOI

Protein ligand structure prediction: From empirical to deep learning approaches.

Current opinion in structural biology Feb 5, 2025
Protein-ligand structure prediction methods, aiming to predict the three-dimensional complex structure and binding energy of a compound and target protein, are essential in many structure-based drug discovery pipelines, including virtual screening an...
Ligands Protein Conformation Proteins Models, Molecular Drug Discovery Protein Binding Computational Biology Deep Learning
View on PubMed DOI

Modern machine learning methods for protein property prediction.

Current opinion in structural biology Jan 28, 2025
Recent progress and development of artificial intelligence and machine learning (AI/ML) techniques have enabled addressing complex biomolecular problems. AI/ML models learn the underlying distribution of data they are trained on and when exposed to n...
Proteins Protein Conformation Machine Learning Computational Biology
View on PubMed DOI
Popular Topics
Recent Journals