AIMC Topic: Models, Molecular

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Prediction of protein structure and AI.

Journal of human genetics Jan 4, 2024
AlphaFold, an artificial intelligence (AI)-based tool for predicting the 3D structure of proteins, is now widely recognized for its high accuracy and versatility in the folding of human proteins. AlphaFold is useful for understanding structure-functi...
Artificial Intelligence Deep Learning Computational Biology Humans Protein Conformation Mutation, Missense Protein Folding Proteins Models, Molecular
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DeepQs: Local quality assessment of cryo-EM density map by deep learning map-model fit score.

Journal of structural biology Dec 30, 2023
Cryogenic electron microscopy maps are valuable for determining macromolecule structures. A proper quality assessment method is essential for cryo-EM map selection or revision. This article presents DeepQs, a novel approach to estimate local quality ...
Microscopy, Electron Protein Conformation Cryoelectron Microscopy Algorithms Deep Learning Models, Molecular
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1,3,4-oxadiazole derivatives: synthesis, characterization, antifungal activity, DNA binding investigations, TD-DFT calculations, and molecular modelling.

Journal of biomolecular structure & dynamics Dec 21, 2023
1,3,4-Oxadiazole-based heterocyclic analogs (3a-3m) were synthesized cyclization of Schiff bases with substituted aldehydes in the presence of bromine and acetic acid. The structural clarification of synthesized molecules was carried out with variou...
Structure-Activity Relationship Microbial Sensitivity Tests Models, Molecular Antifungal Agents DNA Humans Oxadiazoles Antioxidants Molecular Structure Density Functional Theory Molecular Docking Simulation
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De novo design of high-affinity binders of bioactive helical peptides.

Nature Dec 18, 2023
Many peptide hormones form an α-helix on binding their receptors, and sensitive methods for their detection could contribute to better clinical management of disease. De novo protein design can now generate binders with high affinity and specificity ...
Protein Structure, Secondary Glucagon Models, Molecular Luminescent Measurements Parathyroid Hormone Substrate Specificity Peptides Mass Spectrometry Diffusion Proteins Computer-Aided Design Deep Learning Biosensing Techniques
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Bonds and bytes: The odyssey of structural biology.

Current opinion in structural biology Dec 14, 2023
Characterizing structural and dynamic properties of proteins and large macromolecular assemblies is crucial to understand the molecular mechanisms underlying biological functions. In the field of structural biology, no single method comprehensively r...
Artificial Intelligence Computational Biology Proteins Models, Molecular Macromolecular Substances
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Structure, dynamics, and stability of the smallest and most complex 7 protein knot.

The Journal of biological chemistry Dec 10, 2023
Proteins can spontaneously tie a variety of intricate topological knots through twisting and threading of the polypeptide chains. Recently developed artificial intelligence algorithms have predicted several new classes of topological knotted proteins...
Artificial Intelligence Peptides Models, Molecular Protein Structure, Tertiary Bacterial Proteins Ureaplasma urealyticum Protein Folding
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DeepMainmast: integrated protocol of protein structure modeling for cryo-EM with deep learning and structure prediction.

Nature methods Dec 8, 2023
Three-dimensional structure modeling from maps is an indispensable step for studying proteins and their complexes with cryogenic electron microscopy. Although the resolution of determined cryogenic electron microscopy maps has generally improved, the...
Deep Learning Cryoelectron Microscopy Proteins Microscopy, Electron Protein Conformation Models, Molecular
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Role of environmental specificity in CASP results.

BMC bioinformatics Nov 11, 2023
BACKGROUND: Recently, significant progress has been made in the field of protein structure prediction by the application of artificial intelligence techniques, as shown by the results of the CASP13 and CASP14 (Critical Assessment of Structure Predict...
Protein Conformation Protein Folding Models, Molecular Hydrophobic and Hydrophilic Interactions Artificial Intelligence Proteins
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The bad and the good of trends in model building and refinement for sparse-data regions: pernicious forms of overfitting versus good new tools and predictions.

Acta crystallographica. Section D, Structural biology Nov 3, 2023
Model building and refinement, and the validation of their correctness, are very effective and reliable at local resolutions better than about 2.5 Å for both crystallography and cryo-EM. However, at local resolutions worse than 2.5 Å both the procedu...
Artificial Intelligence Peptides Models, Molecular Crystallography, X-Ray Proteins Protein Conformation Cryoelectron Microscopy
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Small-Molecule Conformer Generators: Evaluation of Traditional Methods and AI Models on High-Quality Data Sets.

Journal of chemical information and modeling Oct 26, 2023
Small-molecule conformer generation (SMCG) is an extremely important task in both ligand- and structure-based computer-aided drug design, especially during the hit discovery phase. Recently, a multitude of artificial intelligence (AI) models tailored...
Artificial Intelligence Drug Design Molecular Conformation Models, Molecular Ligands
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