AIMC Topic: Binding Sites

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Deep-learning optimized DEOCSU suite provides an iterable pipeline for accurate ChIP-exo peak calling.

Briefings in bioinformatics Mar 19, 2023
Recognizing binding sites of DNA-binding proteins is a key factor for elucidating transcriptional regulation in organisms. ChIP-exo enables researchers to delineate genome-wide binding landscapes of DNA-binding proteins with near single base-pair res...
Deep Learning Sequence Analysis, DNA Software Algorithms Chromatin Immunoprecipitation Chromatin Immunoprecipitation Sequencing DNA-Binding Proteins Binding Sites
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QuoteTarget: A sequence-based transformer protein language model to identify potentially druggable protein targets.

Protein science : a publication of the Protein Society Feb 1, 2023
The development of efficient computational methods for drug target protein identification can compensate for the high cost of experiments and is therefore of great significance for drug development. However, existing structure-based drug target prote...
Algorithms Proteins Amino Acid Sequence Binding Sites Humans Neural Networks, Computer
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RLBind: a deep learning method to predict RNA-ligand binding sites.

Briefings in bioinformatics Jan 19, 2023
Identification of RNA-small molecule binding sites plays an essential role in RNA-targeted drug discovery and development. These small molecules are expected to be leading compounds to guide the development of new types of RNA-targeted therapeutics c...
Protein Binding RNA Algorithms Deep Learning Ligands Binding Sites
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Annotation of biologically relevant ligands in UniProtKB using ChEBI.

Bioinformatics (Oxford, England) Jan 1, 2023
MOTIVATION: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support effort...
Molecular Sequence Annotation Binding Sites Knowledge Bases Ligands Databases, Protein Amino Acid Sequence
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BindWeb: A web server for ligand binding residue and pocket prediction from protein structures.

Protein science : a publication of the Protein Society Dec 1, 2022
Knowledge of protein-ligand interactions is beneficial for biological process analysis and drug design. Given the complexity of the interactions and the inadequacy of experimental data, accurate ligand binding residue and pocket prediction remains ch...
Ligands Binding Sites Cluster Analysis Proteins Neural Networks, Computer Protein Binding
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CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types.

Bioinformatics (Oxford, England) Sep 30, 2022
MOTIVATION: Three-dimensional (3D) genome organization is of vital importance in gene regulation and disease mechanisms. Previous studies have shown that CTCF-mediated chromatin loops are crucial to studying the 3D structure of cells. Although variou...
Chromatin Cell Line CCCTC-Binding Factor Binding Sites Deep Learning
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HLAncPred: a method for predicting promiscuous non-classical HLA binding sites.

Briefings in bioinformatics Sep 20, 2022
Human leukocyte antigens (HLA) regulate various innate and adaptive immune responses and play a crucial immunomodulatory role. Recent studies revealed that non-classical HLA-(HLA-E & HLA-G) based immunotherapies have many advantages over traditional ...
Protein Binding Spike Glycoprotein, Coronavirus Binding Sites HLA-G Antigens COVID-19 Humans Peptides Artificial Intelligence
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DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors.

Nucleic acids research Sep 9, 2022
We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predi...
Transcription Factors Machine Learning DNA Algorithms Binding Sites Protein Binding
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Identifying modifications on DNA-bound histones with joint deep learning of multiple binding sites in DNA sequence.

Bioinformatics (Oxford, England) Sep 2, 2022
MOTIVATION: Histone modifications are epigenetic markers that impact gene expression by altering the chromatin structure or recruiting histone modifiers. Their accurate identification is key to unraveling the mechanisms by which they regulate gene ex...
DNA Base Sequence Histones Binding Sites Deep Learning Transcription Factors
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CSM-Potential: mapping protein interactions and biological ligands in 3D space using geometric deep learning.

Nucleic acids research Jul 5, 2022
Recent advances in protein structural modelling have enabled the accurate prediction of the holo 3D structures of almost any protein, however protein function is intrinsically linked to the interactions it makes. While a number of computational appro...
Protein Conformation Membrane Proteins Software Binding Sites Protein Interaction Mapping Deep Learning Ligands
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