AIMC Topic: Protein Binding

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ScanNet uncovers binding motifs in protein structures with deep learning.

Nature methods Jun 1, 2022
Binding Sites Nucleotide Motifs Amino Acid Motifs Deep Learning Protein Binding
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PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning.

Bioinformatics (Oxford, England) Apr 12, 2022
MOTIVATION: Protein-RNA interactions play essential roles in many biological processes, including pre-mRNA processing, post-transcriptional gene regulation and RNA degradation. Accurate identification of binding sites on RNA-binding proteins (RBPs) i...
RNA Binding Sites RNA-Binding Proteins Membrane Proteins Protein Binding Deep Learning Computational Biology
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Persistent spectral based ensemble learning (PerSpect-EL) for protein-protein binding affinity prediction.

Briefings in bioinformatics Mar 10, 2022
Protein-protein interactions (PPIs) play a significant role in nearly all cellular and biological activities. Data-driven machine learning models have demonstrated great power in PPIs. However, the design of efficient molecular featurization poses a ...
Protein Binding Neural Networks, Computer Machine Learning
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InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions.

Bioinformatics (Oxford, England) Feb 7, 2022
MOTIVATION: Protein-protein interactions (PPIs) are key elements in numerous biological pathways and the subject of a growing number of drug discovery projects including against infectious diseases. Designing drugs on PPI targets remains a difficult ...
Neural Networks, Computer Drug Design Protein Binding Proteins Binding Sites
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Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning.

Bioinformatics (Oxford, England) Jan 27, 2022
MOTIVATION: In recent years, cyclic peptide drugs have been receiving increasing attention because they can target proteins that are difficult to be tackled by conventional small-molecule drugs or antibody drugs. Plasma protein binding rate (%PPB) is...
Blood Proteins Software Deep Learning Peptides, Cyclic Protein Binding
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Detection of transcription factors binding to methylated DNA by deep recurrent neural network.

Briefings in bioinformatics Jan 17, 2022
Transcription factors (TFs) are proteins specifically involved in gene expression regulation. It is generally accepted in epigenetics that methylated nucleotides could prevent the TFs from binding to DNA fragments. However, recent studies have confir...
Algorithms Protein Binding DNA Methylation Binding Sites Transcription Factors Deep Learning DNA DNA-Binding Proteins Humans Gene Expression Regulation Neural Networks, Computer
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Molecular persistent spectral image (Mol-PSI) representation for machine learning models in drug design.

Briefings in bioinformatics Jan 17, 2022
Artificial intelligence (AI)-based drug design has great promise to fundamentally change the landscape of the pharmaceutical industry. Even though there are great progress from handcrafted feature-based machine learning models, 3D convolutional neura...
Neural Networks, Computer Molecular Structure Ligands Drug Design Models, Theoretical Artificial Intelligence Protein Binding Models, Molecular Machine Learning
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DeepDISOBind: accurate prediction of RNA-, DNA- and protein-binding intrinsically disordered residues with deep multi-task learning.

Briefings in bioinformatics Jan 17, 2022
Proteins with intrinsically disordered regions (IDRs) are common among eukaryotes. Many IDRs interact with nucleic acids and proteins. Annotation of these interactions is supported by computational predictors, but to date, only one tool that predicts...
Humans DNA-Binding Proteins Deep Learning Proteome Computational Biology Intrinsically Disordered Proteins Nucleic Acids Protein Binding RNA DNA RNA-Binding Proteins Neural Networks, Computer
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A point cloud-based deep learning strategy for protein-ligand binding affinity prediction.

Briefings in bioinformatics Jan 17, 2022
There is great interest to develop artificial intelligence-based protein-ligand binding affinity models due to their immense applications in drug discovery. In this paper, PointNet and PointTransformer, two pointwise multi-layer perceptrons have been...
Cloud Computing Artificial Intelligence Deep Learning Protein Binding Ligands
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MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network.

Briefings in bioinformatics Jan 17, 2022
Accurate identification of transcription factor binding sites is of great significance in understanding gene expression, biological development and drug design. Although a variety of methods based on deep-learning models and large-scale data have bee...
Deep Learning Protein Binding Neural Networks, Computer Transcription Factors Binding Sites
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