AIMC Topic: Binding Sites

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RNAProt: an efficient and feature-rich RNA binding protein binding site predictor.

GigaScience Aug 18, 2021
BACKGROUND: Cross-linking and immunoprecipitation followed by next-generation sequencing (CLIP-seq) is the state-of-the-art technique used to experimentally determine transcriptome-wide binding sites of RNA-binding proteins (RBPs). However, it relies...
Protein Binding RNA-Binding Proteins RNA Binding Sites Neural Networks, Computer
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dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains.

Nucleic acids research Jul 21, 2021
Domains are instrumental in facilitating protein interactions with DNA, RNA, small molecules, ions and peptides. Identifying ligand-binding domains within sequences is a critical step in protein function annotation, and the ligand-binding properties ...
Peptides DNA Protein Domains RNA Humans Machine Learning Ions Ligands Binding Sites
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GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues.

Nucleic acids research May 21, 2021
Knowledge of the interactions between proteins and nucleic acids is the basis of understanding various biological activities and designing new drugs. How to accurately identify the nucleic-acid-binding residues remains a challenging task. In this pap...
Binding Sites Software Protein Binding RNA-Binding Proteins DNA DNA-Binding Proteins RNA Protein Conformation Neural Networks, Computer
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Computational Ion Channel Research: from the Application of Artificial Intelligence to Molecular Dynamics Simulations.

Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology Mar 3, 2021
Although ion channels are crucial in many physiological processes and constitute an important class of drug targets, much is still unclear about their function and possible malfunctions that lead to diseases. In recent years, computational methods ha...
Humans Artificial Intelligence Software Ligands Quantitative Structure-Activity Relationship Binding Sites Ion Channels Animals Protein Binding Models, Molecular Molecular Dynamics Simulation Protein Conformation, alpha-Helical Protein Conformation, beta-Strand Membrane Transport Modulators Protein Interaction Domains and Motifs Ion Channel Gating Structural Homology, Protein
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A machine learning-based framework for modeling transcription elongation.

Proceedings of the National Academy of Sciences of the United States of America Feb 9, 2021
RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gen...
Transcription Elongation, Genetic Nucleotide Motifs RNA Splicing RNA Splice Sites HeLa Cells HEK293 Cells Base Sequence Genome, Human Histones Binding Sites RNA Polymerase II Epigenesis, Genetic DNA Methylation Protein Processing, Post-Translational Models, Biological Humans Machine Learning
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Application and assessment of deep learning for the generation of potential NMDA receptor antagonists.

Physical chemistry chemical physics : PCCP Jan 21, 2021
Uncompetitive antagonists of the N-methyl d-aspartate receptor (NMDAR) have demonstrated therapeutic benefit in the treatment of neurological diseases such as Parkinson's and Alzheimer's, but some also cause dissociative effects that have led to the ...
Molecular Structure Ligands Receptors, N-Methyl-D-Aspartate Binding Sites Small Molecule Libraries Xenopus laevis Animals Drug Design Deep Learning Mice
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Predicting regulatory variants using a dense epigenomic mapped CNN model elucidated the molecular basis of trait-tissue associations.

Nucleic acids research Jan 11, 2021
Assessing the causal tissues of human complex diseases is important for the prioritization of trait-associated genetic variants. Yet, the biological underpinnings of trait-associated variants are extremely difficult to infer due to statistical noise ...
Histone Code Humans Epigenome Datasets as Topic Organ Specificity Molecular Sequence Annotation Binding Sites Linkage Disequilibrium Genetic Diseases, Inborn Chromatin Immunoprecipitation Epigenomics Models, Genetic Transcription Factors Causality Deep Learning Genome-Wide Association Study Polymorphism, Single Nucleotide
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Bionoi: A Voronoi Diagram-Based Representation of Ligand-Binding Sites in Proteins for Machine Learning Applications.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2021
Bionoi is a new software to generate Voronoi representations of ligand-binding sites in proteins for machine learning applications. Unlike many other deep learning models in biomedicine, Bionoi utilizes off-the-shelf convolutional neural network arch...
Databases, Chemical Binding Sites Histidine Kinase Drug Discovery Deep Learning Proteins Ligands Neural Networks, Computer Machine Learning Software
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DeepCLIP: predicting the effect of mutations on protein-RNA binding with deep learning.

Nucleic acids research Jul 27, 2020
Nucleotide variants can cause functional changes by altering protein-RNA binding in various ways that are not easy to predict. This can affect processes such as splicing, nuclear shuttling, and stability of the transcript. Therefore, correct modeling...
Base Sequence Nucleic Acid Conformation Binding Sites Nucleotide Motifs RNA-Binding Proteins Mutation RNA Humans Computer Simulation Animals Deep Learning Protein Binding Mice Computational Biology
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Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data.

Bioinformatics (Oxford, England) May 1, 2020
MOTIVATION: Knowledge of protein-ligand binding residues is important for understanding the functions of proteins and their interaction mechanisms. From experimentally solved protein structures, how to accurately identify its potential binding sites ...
Computational Biology Proteins Ligands Binding Sites Machine Learning Algorithms Protein Binding
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