AIMC Topic: Binding Sites

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The prediction of RNA-small molecule binding sites in RNA structures based on geometric deep learning.

International journal of biological macromolecules Apr 21, 2025
Biological interactions between RNA and small-molecule ligands play a crucial role in determining the specific functions of RNA, such as catalysis and folding, and are essential for guiding drug design in the medical field. Accurately predicting the ...
Small Molecule Libraries Nucleic Acid Conformation Binding Sites Deep Learning Computational Biology Models, Molecular RNA Ligands
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TRAPT: a multi-stage fused deep learning framework for predicting transcriptional regulators based on large-scale epigenomic data.

Nature communications Apr 16, 2025
It is challenging to identify regulatory transcriptional regulators (TRs), which control gene expression via regulatory elements and epigenomic signals, in context-specific studies on the onset and progression of diseases. The use of large-scale mult...
Humans Chromatin Deep Learning Computational Biology Gene Expression Regulation Epigenomics Binding Sites Transcription Factors Regulatory Elements, Transcriptional
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Recognition of Specific PIP2-subtype Composition Triggers the Allosteric Control Mechanism for Selective Membrane Targeting of Cargo Loading and Release Functions of the Intracellular Sterol Transporter StarD4.

Journal of molecular biology Apr 15, 2025
We present a comprehensive, quantitative model of the allosteric molecular mechanisms of selective cholesterol (CHL) uptake and delivery by the StarD4 protein - an intracellular cholesterol trafficking protein that facilitates the crucial non-vesicul...
Molecular Dynamics Simulation Biological Transport Cell Membrane Humans Protein Binding Cholesterol Allosteric Regulation Endoplasmic Reticulum Phosphatidylinositol Phosphates Membrane Transport Proteins Binding Sites Sterols
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In silico design of ankyrin repeat proteins that bind to the insulin-like growth factor type 1 receptor.

Journal of molecular graphics & modelling Apr 15, 2025
Ankyrins are proteins widely distributed in nature that mediate protein‒protein interactions. Owing to their outstanding stability and ability to recognize targets, ankyrins have been used as therapeutic and diagnostic tools in several diseases, incl...
Protein Binding Insulin-Like Growth Factor I Receptor, IGF Type 1 Humans Computer Simulation Molecular Docking Simulation Binding Sites Ankyrin Repeat Ankyrins Models, Molecular Amino Acid Sequence Ligands Insulin-Like Peptides
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A comprehensive review of computational methods for Protein-DNA binding site prediction.

Analytical biochemistry Apr 8, 2025
Accurately identifying protein-DNA binding sites is essential for understanding the molecular mechanisms underlying biological processes, which in turn facilitates advancements in drug discovery and design. While biochemical experiments provide the m...
Deep Learning Protein Binding Computational Biology DNA DNA-Binding Proteins Binding Sites Humans Machine Learning
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Deep-ProBind: binding protein prediction with transformer-based deep learning model.

BMC bioinformatics Mar 22, 2025
Binding proteins play a crucial role in biological systems by selectively interacting with specific molecules, such as DNA, RNA, or peptides, to regulate various cellular processes. Their ability to recognize and bind target molecules with high speci...
Proteins Databases, Protein Binding Sites Deep Learning Sequence Analysis, Protein Neural Networks, Computer Protein Binding Algorithms Computational Biology
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PCANN Program for Structure-Based Prediction of Protein-Protein Binding Affinity: Comparison With Other Neural-Network Predictors.

Proteins Mar 21, 2025
In this communication, we introduce a new structure-based affinity predictor for protein-protein complexes. This predictor, dubbed PCANN (Protein Complex Affinity by Neural Network), uses the ESM-2 language model to encode the information about prote...
Protein Binding Computational Biology Proteins Databases, Protein Software Protein Conformation Binding Sites Humans Algorithms Deep Learning Neural Networks, Computer
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RNAmigos2: accelerated structure-based RNA virtual screening with deep graph learning.

Nature communications Mar 21, 2025
RNAs are a vast reservoir of untapped drug targets. Structure-based virtual screening (VS) identifies candidate molecules by leveraging binding site information, traditionally using molecular docking simulations. However, docking struggles to scale w...
Riboswitch Molecular Docking Simulation RNA Deep Learning Nucleic Acid Conformation Binding Sites
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TopEC: prediction of Enzyme Commission classes by 3D graph neural networks and localized 3D protein descriptor.

Nature communications Mar 20, 2025
Tools available for inferring enzyme function from general sequence, fold, or evolutionary information are generally successful. However, they can lead to misclassification if a deviation in local structural features influences the function. Here, we...
Neural Networks, Computer Software Binding Sites Algorithms Enzymes Computational Biology Graph Neural Networks Protein Conformation
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CacPred: a cascaded convolutional neural network for TF-DNA binding prediction.

BMC genomics Mar 18, 2025
BACKGROUND: Transcription factors (TFs) regulate the genes' expression by binding to DNA sequences. Aligned TFBSs of the same TF are seen as cis-regulatory motifs, and substantial computational efforts have been invested to find motifs. In recent yea...
Transcription Factors DNA Binding Sites Chromatin Immunoprecipitation Sequencing Convolutional Neural Networks Protein Binding Computational Biology Neural Networks, Computer Software Algorithms
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