AIMC Topic: Protein Conformation

Clear Filters Showing 131 to 140 of 558 articles

Adaptive Workflows of Machine Learning Illuminate the Sequential Operation Mechanism of the TAK1's Allosteric Network.

Biochemistry May 14, 2024
Allostery is a fundamental mechanism driving biomolecular processes that holds significant therapeutic concern. Our study rigorously investigates how two distinct machine-learning algorithms uniquely classify two already close-to-active DFG-in states...
Allosteric Regulation MAP Kinase Kinase Kinases Machine Learning Algorithms Molecular Dynamics Simulation Protein Conformation Workflow Humans
View on PubMed DOI

Predicting Antimicrobial Peptides Using ESMFold-Predicted Structures and ESM-2-Based Amino Acid Features with Graph Deep Learning.

Journal of chemical information and modeling May 13, 2024
Currently, antimicrobial resistance constitutes a serious threat to human health. Drugs based on antimicrobial peptides (AMPs) constitute one of the alternatives to address it. Shallow and deep learning (DL)-based models have mainly been built from a...
Deep Learning Models, Molecular Protein Conformation Antimicrobial Peptides Amino Acids Amino Acid Sequence
View on PubMed DOI

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 Protein Conformation Antigens Ligands Nucleic Acids Protein Binding Proteins Models, Molecular Molecular Docking Simulation Software Antibodies Deep Learning Reproducibility of Results Ions
View on PubMed DOI

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...
Models, Molecular Protein Conformation Cryoelectron Microscopy Artificial Intelligence Proteins
View on PubMed DOI

Deciphering the Coevolutionary Dynamics of L2 β-Lactamases via Deep Learning.

Journal of chemical information and modeling Apr 30, 2024
L2 β-lactamases, serine-based class A β-lactamases expressed by , play a pivotal role in antimicrobial resistance (AMR). However, limited studies have been conducted on these important enzymes. To understand the coevolutionary dynamics of L2 β-lactam...
Protein Conformation Molecular Dynamics Simulation Stenotrophomonas maltophilia Deep Learning beta-Lactamases Evolution, Molecular
View on PubMed DOI

Generative artificial intelligence for de novo protein design.

Current opinion in structural biology Apr 24, 2024
Engineering new molecules with desirable functions and properties has the potential to extend our ability to engineer proteins beyond what nature has so far evolved. Advances in the so-called 'de novo' design problem have recently been brought forwar...
Protein Engineering Artificial Intelligence Models, Molecular Proteins Protein Conformation
View on PubMed DOI

Machine Learning of Three-Dimensional Protein Structures to Predict the Functional Impacts of Genome Variation.

Journal of chemical information and modeling Apr 18, 2024
Research in the human genome sciences generates a substantial amount of genetic data for hundreds of thousands of individuals, which concomitantly increases the number of variants of unknown significance (VUS). Bioinformatic analyses can successfully...
Genetic Variation Genome, Human NF-E2-Related Factor 2 Proto-Oncogene Proteins c-myc Protein Conformation Humans Computational Biology Machine Learning Models, Molecular
View on PubMed DOI

Encoding the space of protein-protein binding interfaces by artificial intelligence.

Computational biology and chemistry Apr 18, 2024
The physical interactions between proteins are largely determined by the structural properties at their binding interfaces. It was found that the binding interfaces in distinctive protein complexes are highly similar. The structural properties underl...
Artificial Intelligence Models, Molecular Protein Binding Protein Conformation Proteins Binding Sites
View on PubMed DOI

Protein Engineering with Lightweight Graph Denoising Neural Networks.

Journal of chemical information and modeling Apr 17, 2024
Protein engineering faces challenges in finding optimal mutants from a massive pool of candidate mutants. In this study, we introduce a deep-learning-based data-efficient fitness prediction tool to steer protein engineering. Our methodology establish...
Protein Engineering Mutation Protein Conformation Neural Networks, Computer Proteins Deep Learning Models, Molecular
View on PubMed DOI

Apprehensions and emerging solutions in ML-based protein structure prediction.

Current opinion in structural biology Apr 16, 2024
The three-dimensional structure of proteins determines their function in vital biological processes. Thus, when the structure is known, the molecular mechanism of protein function can be understood in more detail and obtained information utilized in ...
Protein Conformation Proteins Machine Learning Models, Molecular Computational Biology
View on PubMed DOI
Popular Topics
Recent Journals