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Models, Molecular

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Consistent semantic representation learning for out-of-distribution molecular property prediction.

Briefings in bioinformatics 40205853
Invariant molecular representation models provide potential solutions to guarantee accurate prediction of molecular properties under distribution shifts out-of-distribution (OOD) by identifying and leveraging invariant substructures inherent to the m...
Algorithms Computational Biology Machine Learning Models, Molecular Semantics
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Critical Assessment of RNA and DNA Structure Predictions via Artificial Intelligence: The Imitation Game.

Journal of chemical information and modeling 40159092
Computational predictions of biomolecular structure via artificial intelligence (AI) based approaches, as exemplified by AlphaFold software, have the potential to model of all life's biomolecules. We performed oligonucleotide structure prediction and...
Artificial Intelligence DNA Models, Molecular Nucleic Acid Conformation RNA
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Atomic context-conditioned protein sequence design using LigandMPNN.

Nature methods 40155723
Protein sequence design in the context of small molecules, nucleotides and metals is critical to enzyme and small-molecule binder and sensor design, but current state-of-the-art deep-learning-based sequence design methods are unable to model nonprote...
Amino Acid Sequence Crystallography, X-Ray Deep Learning Ligands Models, Molecular Protein Binding Protein Conformation Proteins
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Fitting Atomic Structures into Cryo-EM Maps by Coupling Deep Learning-Enhanced Map Processing with Global-Local Optimization.

Journal of chemical information and modeling 40152222
With the breakthroughs in protein structure prediction technology, constructing atomic structures from cryo-electron microscopy (cryo-EM) density maps through structural fitting has become increasingly critical. However, the accuracy of the construct...
Cryoelectron Microscopy Deep Learning Models, Molecular Protein Conformation Proteins
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Comparing Explanations of Molecular Machine Learning Models Generated with Different Methods for the Calculation of Shapley Values.

Molecular informatics 40112199
Feature attribution methods from explainable artificial intelligence (XAI) provide explanations of machine learning models by quantifying feature importance for predictions of test instances. While features determining individual predictions have fre...
Algorithms Artificial Intelligence Machine Learning Models, Molecular
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TopoQA: a topological deep learning-based approach for protein complex structure interface quality assessment.

Briefings in bioinformatics 40062613
Even with the significant advances of AlphaFold-Multimer (AF-Multimer) and AlphaFold3 (AF3) in protein complex structure prediction, their accuracy is still not comparable with monomer structure prediction. Efficient and effective quality assessment ...
Computational Biology Databases, Protein Deep Learning Models, Molecular Molecular Docking Simulation Neural Networks, Computer Protein Conformation Proteins Software
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Deep learning tools predict variants in disordered regions with lower sensitivity.

BMC genomics 40221640
BACKGROUND: The recent AI breakthrough of AlphaFold2 has revolutionized 3D protein structural modeling, proving crucial for protein design and variant effects prediction. However, intrinsically disordered regions-known for their lack of well-defined ...
Computational Biology Deep Learning Humans Intrinsically Disordered Proteins Methionine Models, Molecular Mutation Protein Conformation, alpha-Helical Proteome
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Unified Deep Learning of Molecular and Protein Language Representations with T5ProtChem.

Journal of chemical information and modeling 40197028
Deep learning has revolutionized difficult tasks in chemistry and biology, yet existing language models often treat these domains separately, relying on concatenated architectures and independently pretrained weights. These approaches fail to fully e...
Computational Biology Deep Learning Drug Discovery Models, Molecular Proteins
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Machine learning models for predicting configuration of modified knuckle epitope peptides of BMP-2 protein using mesoscale simulation data.

Physical chemistry chemical physics : PCCP 40183939
The high doses of bone morphogenetic proteins (BMPs) cause undesired side effects in skeletal tissue regeneration. An alternative approach is to use the bioactive knuckle epitope domain of BMP-2 (BMP2-KEP) with an open-arm structure as part of the pr...
Amino Acid Sequence Bone Morphogenetic Protein 2 Epitopes Humans Machine Learning Models, Molecular Peptides Quantitative Structure-Activity Relationship
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A Specialized and Enhanced Deep Generation Model for Active Molecular Design Targeting Kinases Guided by Affinity Prediction Models and Reinforcement Learning.

Journal of chemical information and modeling 40175286
Kinases are critical regulators in numerous cellular processes, and their dysregulation is linked to various diseases, including cancer. Thus, protein kinases have emerged as major drug targets at present, with approximately a quarter to a third of g...
Deep Learning Drug Design Models, Molecular Protein Kinase Inhibitors Protein Kinases
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