AIMC Topic: Binding Sites

Clear Filters Showing 431 to 440 of 500 articles

GRaSP-web: a machine learning strategy to predict binding sites based on residue neighborhood graphs.

Nucleic acids research Jul 5, 2022
Proteins are essential macromolecules for the maintenance of living systems. Many of them perform their function by interacting with other molecules in regions called binding sites. The identification and characterization of these regions are of fund...
Machine Learning Protein Domains Ligands Protein Binding Binding Sites Proteins
View on PubMed DOI

ScanNet uncovers binding motifs in protein structures with deep learning.

Nature methods Jun 1, 2022
Amino Acid Motifs Binding Sites Nucleotide Motifs Deep Learning Protein Binding
View on PubMed DOI

PST-PRNA: prediction of RNA-binding sites using protein surface topography and deep learning.

Bioinformatics (Oxford, England) Apr 12, 2022
MOTIVATION: Protein-RNA interactions play essential roles in many biological processes, including pre-mRNA processing, post-transcriptional gene regulation and RNA degradation. Accurate identification of binding sites on RNA-binding proteins (RBPs) i...
Binding Sites Membrane Proteins Deep Learning Computational Biology Protein Binding RNA-Binding Proteins RNA
View on PubMed DOI

DNAcycP: a deep learning tool for DNA cyclizability prediction.

Nucleic acids research Apr 8, 2022
DNA mechanical properties play a critical role in every aspect of DNA-dependent biological processes. Recently a high throughput assay named loop-seq has been developed to quantify the intrinsic bendability of a massive number of DNA fragments simult...
DNA Mammals Deep Learning Mice Chromatin Nucleosomes Cyclization Saccharomyces cerevisiae Binding Sites Software Animals
View on PubMed DOI

InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions.

Bioinformatics (Oxford, England) Feb 7, 2022
MOTIVATION: Protein-protein interactions (PPIs) are key elements in numerous biological pathways and the subject of a growing number of drug discovery projects including against infectious diseases. Designing drugs on PPI targets remains a difficult ...
Proteins Binding Sites Drug Design Protein Binding Neural Networks, Computer
View on PubMed DOI

Detection of transcription factors binding to methylated DNA by deep recurrent neural network.

Briefings in bioinformatics Jan 17, 2022
Transcription factors (TFs) are proteins specifically involved in gene expression regulation. It is generally accepted in epigenetics that methylated nucleotides could prevent the TFs from binding to DNA fragments. However, recent studies have confir...
Binding Sites DNA-Binding Proteins Gene Expression Regulation Algorithms DNA Methylation Humans Protein Binding Deep Learning DNA Neural Networks, Computer Transcription Factors
View on PubMed DOI

Protein-RNA interaction prediction with deep learning: structure matters.

Briefings in bioinformatics Jan 17, 2022
Protein-RNA interactions are of vital importance to a variety of cellular activities. Both experimental and computational techniques have been developed to study the interactions. Because of the limitation of the previous database, especially the lac...
Algorithms RNA-Binding Proteins RNA Protein Conformation Binding Sites Deep Learning Computational Biology
View on PubMed DOI

MAResNet: predicting transcription factor binding sites by combining multi-scale bottom-up and top-down attention and residual network.

Briefings in bioinformatics Jan 17, 2022
Accurate identification of transcription factor binding sites is of great significance in understanding gene expression, biological development and drug design. Although a variety of methods based on deep-learning models and large-scale data have bee...
Neural Networks, Computer Deep Learning Transcription Factors Protein Binding Binding Sites
View on PubMed DOI

Assessing deep learning methods in cis-regulatory motif finding based on genomic sequencing data.

Briefings in bioinformatics Jan 17, 2022
Identifying cis-regulatory motifs from genomic sequencing data (e.g. ChIP-seq and CLIP-seq) is crucial in identifying transcription factor (TF) binding sites and inferring gene regulatory mechanisms for any organism. Since 2015, deep learning (DL) me...
Algorithms Deep Learning Binding Sites Transcription Factors Chromatin Immunoprecipitation Base Sequence
View on PubMed DOI

circRNA-binding protein site prediction based on multi-view deep learning, subspace learning and multi-view classifier.

Briefings in bioinformatics Jan 17, 2022
Circular RNAs (circRNAs) generally bind to RNA-binding proteins (RBPs) to play an important role in the regulation of autoimmune diseases. Thus, it is crucial to study the binding sites of RBPs on circRNAs. Although many methods, including traditiona...
RNA, Circular Humans Deep Learning Carrier Proteins Computational Biology Binding Sites
View on PubMed DOI
Popular Topics
Recent Journals