AIMC Topic: Binding Sites

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AttentionDTA: Drug-Target Binding Affinity Prediction by Sequence-Based Deep Learning With Attention Mechanism.

IEEE/ACM transactions on computational biology and bioinformatics Apr 3, 2023
The identification of drug-target relations (DTRs) is substantial in drug development. A large number of methods treat DTRs as drug-target interactions (DTIs), a binary classification problem. The main drawback of these methods are the lack of reliab...
Drug Development Amino Acid Sequence Binding Sites Deep Learning
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How Deepbics Quantifies Intensities of Transcription Factor-DNA Binding and Facilitates Prediction of Single Nucleotide Variant Pathogenicity With a Deep Learning Model Trained On ChIP-Seq Data Sets.

IEEE/ACM transactions on computational biology and bioinformatics Apr 3, 2023
The binding of DNA sequences to cell type-specific transcription factors is essential for regulating gene expression in all organisms. Many variants occurring in these binding regions play crucial roles in human disease by disrupting the cis-regulati...
Transcription Factors DNA Deep Learning Humans Binding Sites Virulence Chromatin Immunoprecipitation Sequencing Nucleotides
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Deep Learning-Based Modeling of Drug-Target Interaction Prediction Incorporating Binding Site Information of Proteins.

Interdisciplinary sciences, computational life sciences Mar 26, 2023
Chemogenomics, also known as proteochemometrics, covers various computational methods for predicting interactions between related drugs and targets on large-scale data. Chemogenomics is used in the early stages of drug discovery to predict the off-ta...
Deep Learning Proteins Machine Learning Drug Discovery Binding Sites Ligands
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Assessing protein homology models with docking reproducibility.

Journal of molecular graphics & modelling Feb 11, 2023
Results of the recent Critical Assessment of Protein Structure (CASP) competitions demonstrate that protein backbones can be predicted with very high accuracy. In particular, the artificial intelligence methods of AlphaFold 2 from DeepMind were able ...
Binding Sites Ligands Protein Conformation Proteins Artificial Intelligence Reproducibility of Results Protein Binding
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DapNet-HLA: Adaptive dual-attention mechanism network based on deep learning to predict non-classical HLA binding sites.

Analytical biochemistry Feb 3, 2023
Human leukocyte antigen (HLA) plays a vital role in immunomodulatory function. Studies have shown that immunotherapy based on non-classical HLA has essential applications in cancer, COVID-19, and allergic diseases. However, there are few deep learnin...
Histocompatibility Antigens Class I Binding Sites HLA Antigens Humans COVID-19 Deep Learning
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Learning the protein language of proteome-wide protein-protein binding sites via explainable ensemble deep learning.

Communications biology Jan 19, 2023
Protein-protein interactions (PPIs) govern cellular pathways and processes, by significantly influencing the functional expression of proteins. Therefore, accurate identification of protein-protein interaction binding sites has become a key step in t...
Algorithms Binding Sites Protein Binding Proteome Deep Learning
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DeepBSRPred: deep learning-based binding site residue prediction for proteins.

Amino acids Dec 27, 2022
MOTIVATION: Proteins-protein interactions (PPIs) are important to govern several cellular activities. Amino acid residues, which are located at the interface are known as the binding sites and the information about binding sites helps to understand t...
Proteins Amino Acids Binding Sites Software Deep Learning
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Improved compound-protein interaction site and binding affinity prediction using self-supervised protein embeddings.

BMC bioinformatics Dec 16, 2022
BACKGROUND: Compound-protein interaction site and binding affinity predictions are crucial for drug discovery and drug design. In recent years, many deep learning-based methods have been proposed for predications related to compound-protein interacti...
Proteins Amino Acid Sequence Binding Sites Neural Networks, Computer Drug Discovery
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Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics Dec 8, 2022
Identification of transcription factor binding sites (TFBSs) is essential for revealing the rules of protein-DNA binding. Although some computational methods have been presented to predict TFBSs using epigenomic and sequence features, most of them ig...
Transcription Factors Binding Sites Protein Binding Neural Networks, Computer Algorithms
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Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network.

Journal of chemical information and modeling Nov 7, 2022
The analysis and comparison of protein-binding sites aid various applications in the drug discovery process, e.g., hit finding, drug repurposing, and polypharmacology. Classification of binding sites has been a hot topic for the past 30 years, and ma...
Proteins Binding Sites Machine Learning Neural Networks, Computer Protein Binding
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