AIMC Topic: Binding Sites

Clear Filters Showing 161 to 170 of 499 articles

ScanNet: an interpretable geometric deep learning model for structure-based protein binding site prediction.

Nature methods May 30, 2022
Predicting the functional sites of a protein from its structure, such as the binding sites of small molecules, other proteins or antibodies, sheds light on its function in vivo. Currently, two classes of methods prevail: machine learning models built...
Humans COVID-19 Proteins Binding Sites Protein Binding Spike Glycoprotein, Coronavirus SARS-CoV-2 Deep Learning
View on PubMed DOI

Prediction of protein-ligand binding affinity from sequencing data with interpretable machine learning.

Nature biotechnology May 23, 2022
Protein-ligand interactions are increasingly profiled at high throughput using affinity selection and massively parallel sequencing. However, these assays do not provide the biophysical parameters that most rigorously quantify molecular interactions....
Binding Sites Chromatin Immunoprecipitation DNA Ligands Protein Binding Machine Learning Transcription Factors
View on PubMed DOI

Differences in ligand-induced protein dynamics extracted from an unsupervised deep learning approach correlate with protein-ligand binding affinities.

Communications biology May 19, 2022
Prediction of protein-ligand binding affinity is a major goal in drug discovery. Generally, free energy gap is calculated between two states (e.g., ligand binding and unbinding). The energy gap implicitly includes the effects of changes in protein dy...
Proteins Deep Learning Ligands Protein Binding Binding Sites
View on PubMed DOI

DeepBtoD: Improved RNA-binding proteins prediction via integrated deep learning.

Journal of bioinformatics and computational biology Apr 21, 2022
RNA-binding proteins (RBPs) have crucial roles in various cellular processes such as alternative splicing and gene regulation. Therefore, the analysis and identification of RBPs is an essential issue. However, although many computational methods have...
Binding Sites Protein Binding Computational Biology RNA Base Sequence RNA-Binding Proteins Deep Learning
View on PubMed DOI

Prediction of the transcription factor binding sites with meta-learning.

Methods (San Diego, Calif.) Apr 21, 2022
With the accumulation of ChIP-seq data, convolution neural network (CNN)-based methods have been proposed for predicting transcription factor binding sites (TFBSs). However, biological experimental data are noisy, and are often treated as ground trut...
Neural Networks, Computer Protein Binding Chromatin Immunoprecipitation Sequencing Transcription Factors Binding Sites
View on PubMed DOI

FCNGRU: Locating Transcription Factor Binding Sites by Combing Fully Convolutional Neural Network With Gated Recurrent Unit.

IEEE journal of biomedical and health informatics Apr 14, 2022
Deciphering the relationship between transcription factors (TFs) and DNA sequences is very helpful for computational inference of gene regulation and a comprehensive understanding of gene regulation mechanisms. Transcription factor binding sites (TFB...
Computational Biology Transcription Factors Neural Networks, Computer Protein Binding Binding Sites DNA Nucleotides Humans
View on PubMed DOI

Chromatin interaction-aware gene regulatory modeling with graph attention networks.

Genome research Apr 8, 2022
Linking distal enhancers to genes and modeling their impact on target gene expression are longstanding unresolved problems in regulatory genomics and critical for interpreting noncoding genetic variation. Here, we present a new deep learning approach...
Gene Expression Regulation Binding Sites Chromatin Regulatory Sequences, Nucleic Acid Gene Regulatory Networks Transcription Factors Neural Networks, Computer
View on PubMed DOI

Affinity prediction using deep learning based on SMILES input for D3R grand challenge 4.

Journal of computer-aided molecular design Mar 22, 2022
Modern molecular docking comprises the prediction of pose and affinity. Prediction of docking poses is required for affinity prediction when three-dimensional coordinates of the ligand have not been provided. However, a large number of feature engine...
Deep Learning Protein Binding Molecular Docking Simulation Drug Design Thermodynamics Proteins Ligands Humans Databases, Protein Protein Conformation Binding Sites
View on PubMed DOI

BIPSPI+: Mining Type-Specific Datasets of Protein Complexes to Improve Protein Binding Site Prediction.

Journal of molecular biology Mar 21, 2022
Computational approaches for predicting protein-protein interfaces are extremely useful for understanding and modelling the quaternary structure of protein assemblies. In particular, partner-specific binding site prediction methods allow delineating ...
Datasets as Topic Protein Binding Machine Learning Proteins Software Internet Use Binding Sites Protein Interaction Mapping
View on PubMed DOI

Predicting residues involved in anti-DNA autoantibodies with limited neural networks.

Medical & biological engineering & computing Mar 18, 2022
Computer-aided rational vaccine design (RVD) and synthetic pharmacology are rapidly developing fields that leverage existing datasets for developing compounds of interest. Computational proteomics utilizes algorithms and models to probe proteins for ...
DNA Autoantibodies Algorithms Binding Sites Proteins Neural Networks, Computer
View on PubMed DOI
Popular Topics
Recent Journals