AIMC Topic: Binding Sites

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Predicting Conserved Water Molecules in Binding Sites of Proteins Using Machine Learning Methods and Combining Features.

Computational and mathematical methods in medicine Oct 3, 2022
Water molecules play an important role in many biological processes in terms of stabilizing protein structures, assisting protein folding, and improving binding affinity. It is well known that, due to the impacts of various environmental factors, it ...
Binding Sites Support Vector Machine Proteins Bayes Theorem Solvents Machine Learning Water Humans
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TAMC: A deep-learning approach to predict motif-centric transcriptional factor binding activity based on ATAC-seq profile.

PLoS computational biology Sep 12, 2022
Determining transcriptional factor binding sites (TFBSs) is critical for understanding the molecular mechanisms regulating gene expression in different biological conditions. Biological assays designed to directly mapping TFBSs require large sample s...
Deep Learning Binding Sites Chromatin Immunoprecipitation Sequencing Protein Binding Transcription Factors
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Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning.

Journal of chemical information and modeling Aug 30, 2022
The mechanism of transcriptional activation/repression of the nuclear receptors (NRs) involves two main conformations of the NR protein, namely, the active (agonistic) and inactive (antagonistic) conformations. Binding of agonists or antagonists to t...
Binding Sites Ligands Machine Learning Receptors, Cytoplasmic and Nuclear
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Deep Learning-Based Label-Free Surface-Enhanced Raman Scattering Screening and Recognition of Small-Molecule Binding Sites in Proteins.

Analytical chemistry Aug 15, 2022
Identification of small-molecule binding sites in proteins is of great significance in analysis of protein function and drug design. Modified sites can be recognized via proteolytic cleavage followed by liquid chromatography-mass spectrometry (LC-MS)...
Binding Sites Proteins Tandem Mass Spectrometry Peptides Deep Learning Spectrum Analysis, Raman
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iDRBP-ECHF: Identifying DNA- and RNA-binding proteins based on extensible cubic hybrid framework.

Computers in biology and medicine Aug 13, 2022
Proteins interact with nucleic acids to regulate the life activities of organisms. Therefore, how to accurately and efficiently identify nucleic acid-binding proteins (NABPs) is particularly significant. Some sequence-based computational methods have...
Machine Learning Algorithms DNA DNA-Binding Proteins Computational Biology RNA-Binding Proteins Binding Sites
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Predicting RBP Binding Sites of RNA With High-Order Encoding Features and CNN-BLSTM Hybrid Model.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
RNA binding protein (RBP) is extensively involved in various cellular regulatory processes through the interaction with RNAs. Capturing the RBP binding preferences is fundamental for revealing the pathogenesis of complex diseases. Many experimental d...
RNA Binding Sites Neural Networks, Computer Protein Binding RNA-Binding Proteins
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GraphSite: Ligand Binding Site Classification with Deep Graph Learning.

Biomolecules Jul 29, 2022
The binding of small organic molecules to protein targets is fundamental to a wide array of cellular functions. It is also routinely exploited to develop new therapeutic strategies against a variety of diseases. On that account, the ability to effect...
Binding Sites Neural Networks, Computer Proteins Ligands Artificial Intelligence Molecular Docking Simulation
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Prediction of protein mononucleotide binding sites using AlphaFold2 and machine learning.

Computational biology and chemistry Jul 23, 2022
In this study, we developed a system that predicts the binding sites of proteins for five mononucleotides (AMP, ADP, ATP, GDP, and GTP). The system comprises two machine learning (ML)-based predictors using a convolutional neural network and a gradie...
Machine Learning Protein Binding Proteins Adenosine Monophosphate Binding Sites Adenosine Triphosphate Adenosine Diphosphate Ligands
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ScanNet: A Web Server for Structure-based Prediction of Protein Binding Sites with Geometric Deep Learning.

Journal of molecular biology Jul 22, 2022
Predicting the various binding sites of a protein from its structure sheds light on its function and paves the way towards design of interaction inhibitors. Here, we report ScanNet, a freely available web server for prediction of protein-protein, pro...
Deep Learning Software Internet Use Proteins Protein Binding Binding Sites
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Scaffolding protein functional sites using deep learning.

Science (New York, N.Y.) Jul 21, 2022
The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without n...
Protein Folding Protein Engineering Protein Structure, Secondary Catalysis Binding Sites Deep Learning Protein Binding Proteins
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