AIMC Topic: Protein Binding

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An in vitro and machine learning framework for quantifying serum albumin binding of per- and polyfluoroalkyl substances.

Toxicological sciences : an official journal of the Society of Toxicology Jan 1, 2025
Per- and polyfluoroalkyl substances (PFAS) are a diverse class of anthropogenic chemicals; many are persistent, bioaccumulative, and mobile in the environment. Worldwide, PFAS bioaccumulation causes serious adverse health impacts, yet the physiochemi...
Environmental Pollutants Fluorocarbons Serum Albumin, Human Humans Machine Learning Protein Binding
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TPepRet: a deep learning model for characterizing T-cell receptors-antigen binding patterns.

Bioinformatics (Oxford, England) Dec 26, 2024
MOTIVATION: T-cell receptors (TCRs) elicit and mediate the adaptive immune response by recognizing antigenic peptides, a process pivotal for cancer immunotherapy, vaccine design, and autoimmune disease management. Understanding the intricate binding ...
Humans COVID-19 Receptors, Antigen, T-Cell Protein Binding Computational Biology SARS-CoV-2 Peptides Deep Learning
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Improving generalizability of drug-target binding prediction by pre-trained multi-view molecular representations.

Bioinformatics (Oxford, England) Dec 26, 2024
MOTIVATION: Most drugs start on their journey inside the body by binding the right target proteins. This is the reason that numerous efforts have been devoted to predicting the drug-target binding during drug development. However, the inherent divers...
Proteins Binding Sites Drug Discovery Humans Protein Binding Neural Networks, Computer Computational Biology
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Examining the Influenza A Virus Sialic Acid Binding Preference Predictions of a Sequence-Based Convolutional Neural Network.

Influenza and other respiratory viruses Dec 1, 2024
BACKGROUND: Though receptor binding specificity is well established as a contributor to host tropism and spillover potential of influenza A viruses, determining receptor binding preference of a specific virus still requires expensive and time-consumi...
Hemagglutinin Glycoproteins, Influenza Virus Receptors, Virus N-Acetylneuraminic Acid Protein Binding Amino Acid Sequence Influenza, Human Humans Neural Networks, Computer Machine Learning Influenza A virus
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Attention-aware differential learning for predicting peptide-MHC class I binding and T cell receptor recognition.

Briefings in bioinformatics Nov 22, 2024
The identification of neoantigens is crucial for advancing vaccines, diagnostics, and immunotherapies. Despite this importance, a fundamental question remains: how to model the presentation of neoantigens by major histocompatibility complex class I m...
Computational Biology Histocompatibility Antigens Class I Receptors, Antigen, T-Cell Protein Binding Humans Machine Learning Algorithms Peptides
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EuDockScore: Euclidean graph neural networks for scoring protein-protein interfaces.

Bioinformatics (Oxford, England) Nov 1, 2024
MOTIVATION: Protein-protein interactions are essential for a variety of biological phenomena including mediating biochemical reactions, cell signaling, and the immune response. Proteins seek to form interfaces which reduce overall system energy. Alth...
Protein Interaction Mapping Proteins Protein Conformation Software Algorithms Molecular Docking Simulation Deep Learning Neural Networks, Computer Protein Binding Computational Biology
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Predicting bacterial transcription factor binding sites through machine learning and structural characterization based on DNA duplex stability.

Briefings in bioinformatics Sep 23, 2024
Transcriptional factors (TFs) in bacteria play a crucial role in gene regulation by binding to specific DNA sequences, thereby assisting in the activation or repression of genes. Despite their central role, deciphering shape recognition of bacterial ...
Machine Learning Algorithms Protein Binding Bacteria Nucleic Acid Conformation Binding Sites Transcription Factors Computational Biology DNA, Bacterial DNA Bacterial Proteins
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Machine learning enables pan-cancer identification of mutational hotspots at persistent CTCF binding sites.

Nucleic acids research Aug 12, 2024
CCCTC-binding factor (CTCF) is an insulator protein that binds to a highly conserved DNA motif and facilitates regulation of three-dimensional (3D) nuclear architecture and transcription. CTCF binding sites (CTCF-BSs) reside in non-coding DNA and are...
Chromatin CCCTC-Binding Factor Prostatic Neoplasms Mutation Binding Sites Female Neoplasms Breast Neoplasms Protein Binding Humans Male Machine Learning
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Machine learning-assisted substrate binding pocket engineering based on structural information.

Briefings in bioinformatics Jul 25, 2024
Engineering enzyme-substrate binding pockets is the most efficient approach for modifying catalytic activity, but is limited if the substrate binding sites are indistinct. Here, we developed a 3D convolutional neural network for predicting protein-li...
Ligands Acid Phosphatase Substrate Specificity Protein Binding Klebsiella Protein Engineering Neural Networks, Computer Models, Molecular Binding Sites Bacillus anthracis Machine Learning Bacterial Proteins
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[Advances in using artificial intelligence for predicting protein-ligand binding affinity].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology Jul 25, 2024
The binding of proteins and ligands is a crucial aspect of life processes. The calculation of the protein-ligand binding affinity (PLBA) offers valuable insights into protein function, drug screening targets protein receptors, and enzyme modification...
Algorithms Protein Binding Proteins Artificial Intelligence Ligands
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