AIMC Topic: Proteins

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PDB-IHM: A System for Deposition, Curation, Validation, and Dissemination of Integrative Structures.

Journal of molecular biology Jan 27, 2025
Structures of many large biomolecular assemblies are now being determined using integrative approaches. In these approaches, information derived from multiple experimental and computational methods is combined to compute three-dimensional structures ...
Software Models, Molecular Computational Biology Proteins Protein Conformation Databases, Protein Data Curation
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MAI-TargetFisher: A proteome-wide drug target prediction method synergetically enhanced by artificial intelligence and physical modeling.

Acta pharmacologica Sinica Jan 27, 2025
Computational target identification plays a pivotal role in the drug development process. With the significant advancements of deep learning methods for protein structure prediction, the structural coverage of human proteome has increased substantial...
Binding Sites Proteins Databases, Protein Drug Discovery Humans Artificial Intelligence Proteome Algorithms
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Transformer Decoder Learns from a Pretrained Protein Language Model to Generate Ligands with High Affinity.

Journal of chemical information and modeling Jan 27, 2025
The drug discovery process can be significantly accelerated by using deep learning methods to suggest molecules with druglike features and, more importantly, that are good candidates to bind specific proteins of interest. We present a novel deep lear...
Protein Binding Proteins Drug Discovery Deep Learning Models, Molecular Ligands
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Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning.

PLoS computational biology Jan 24, 2025
The "similarity of dissimilarities" is an emerging paradigm in biomedical science with significant implications for protein function prediction, machine learning (ML), and personalized medicine. In protein function prediction, recognizing dissimilari...
Humans Algorithms Precision Medicine Machine Learning Computational Biology Proteins
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Phyre2.2: A Community Resource for Template-based Protein Structure Prediction.

Journal of molecular biology Jan 23, 2025
Template-based modelling, also known as homology modelling, is a powerful approach to predict the structure of a protein from its amino acid sequence. The approach requires one to identify a sequence similarity between the query sequence and that of ...
Protein Conformation Models, Molecular Amino Acid Sequence Software Proteins Computational Biology Databases, Protein
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GraphPhos: Predict Protein-Phosphorylation Sites Based on Graph Neural Networks.

International journal of molecular sciences Jan 23, 2025
Phosphorylation is one of the most common protein post-translational modifications. The identification of phosphorylation sites serves as the cornerstone for protein-phosphorylation-related research. This paper proposes a protein-phosphorylation site...
Protein Processing, Post-Translational Algorithms Neural Networks, Computer Computational Biology Proteins Software Amino Acid Sequence Phosphorylation Graph Neural Networks
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Deep learning methods for proteome-scale interaction prediction.

Current opinion in structural biology Jan 22, 2025
Proteome-scale interaction prediction is essential for understanding protein functions and disease mechanisms. Traditional experimental methods are often limited by scale and complexity, driving the need for computational approaches. Deep learning ha...
Protein Interaction Mapping Deep Learning Protein Binding Proteome Proteins Computational Biology Humans
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MVGNN-PPIS: A novel multi-view graph neural network for protein-protein interaction sites prediction based on Alphafold3-predicted structures and transfer learning.

International journal of biological macromolecules Jan 21, 2025
Protein-protein interactions (PPI) are crucial for understanding numerous biological processes and pathogenic mechanisms. Identifying interaction sites is essential for biomedical research and targeted drug development. Compared to experimental metho...
Graph Neural Networks Binding Sites Protein Interaction Mapping Protein Binding Neural Networks, Computer Models, Molecular Computational Biology Proteins Algorithms Protein Conformation
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Deciphering Protein Secondary Structures and Nucleic Acids in Cryo-EM Maps Using Deep Learning.

Journal of chemical information and modeling Jan 21, 2025
With the resolution revolution of cryo-electron microscopy (cryo-EM) and the rapid development of image processing technology, cryo-EM has become an indispensable experimental method for determining the three-dimensional structures of biological macr...
Proteins Models, Molecular Deep Learning Protein Structure, Secondary Nucleic Acids Cryoelectron Microscopy
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MMPD-DTA: Integrating Multi-Modal Deep Learning with Pocket-Drug Graphs for Drug-Target Binding Affinity Prediction.

Journal of chemical information and modeling Jan 20, 2025
Predicting drug-target binding affinity (DTA) is a crucial task in drug discovery research. Recent studies have demonstrated that pocket features and interactions between targets and drugs significantly improve the understanding of DTA. However, chal...
Humans Drug Discovery Binding Sites Proteins Pharmaceutical Preparations Deep Learning Protein Binding
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