AIMC Topic: Binding Sites

Clear Filters Showing 411 to 420 of 500 articles

CheRRI-Accurate classification of the biological relevance of putative RNA-RNA interaction sites.

GigaScience Jan 2, 2024
BACKGROUND: RNA-RNA interactions are key to a wide range of cellular functions. The detection of potential interactions helps to understand the underlying processes. However, potential interactions identified via in silico or experimental high-throug...
Humans RNA Machine Learning Binding Sites Software Computational Biology
View on PubMed DOI

Estimating protein-ligand interactions with geometric deep learning and mixture density models.

Journal of biosciences Jan 1, 2024
Understanding the interactions between a ligand and its molecular target is crucial in guiding the optimization of molecules for any drug design workflow. Multiple experimental and computational methods have been developed to better understand these...
Drug Design Deep Learning Algorithms Molecular Docking Simulation Ligands Protein Conformation Binding Sites Protein Binding Proteins Neural Networks, Computer
View on PubMed

Peptidic Compound as DNA Binding Agent: Fragment-based Design, Machine Learning, Molecular Modeling, Synthesis, and DNA Binding Evaluation.

Protein and peptide letters Jan 1, 2024
BACKGROUND: Cancer remains a global burden, with increasing mortality rates. Current cancer treatments involve controlling the transcription of malignant DNA genes, either directly or indirectly. DNA exhibits various structural forms, including the G...
Machine Learning Computer Simulation Humans Protein Binding DNA Peptides Molecular Docking Simulation Drug Design Antineoplastic Agents G-Quadruplexes Binding Sites Molecular Dynamics Simulation
View on PubMed DOI

ProteinMAE: masked autoencoder for protein surface self-supervised learning.

Bioinformatics (Oxford, England) Dec 1, 2023
SUMMARY: The biological functions of proteins are determined by the chemical and geometric properties of their surfaces. Recently, with the booming progress of deep learning, a series of learning-based surface descriptors have been proposed and achie...
Protein Domains Supervised Machine Learning Binding Sites Membrane Proteins Natural Language Processing
View on PubMed DOI

Unraveling viral drug targets: a deep learning-based approach for the identification of potential binding sites.

Briefings in bioinformatics Nov 22, 2023
The coronavirus disease 2019 (COVID-19) pandemic has spurred a wide range of approaches to control and combat the disease. However, selecting an effective antiviral drug target remains a time-consuming challenge. Computational methods offer a promisi...
Molecular Dynamics Simulation Binding Sites SARS-CoV-2 Humans Deep Learning COVID-19 Protein Binding Antibodies, Viral Spike Glycoprotein, Coronavirus
View on PubMed DOI

Accurately identifying nucleic-acid-binding sites through geometric graph learning on language model predicted structures.

Briefings in bioinformatics Sep 22, 2023
The interactions between nucleic acids and proteins are important in diverse biological processes. The high-quality prediction of nucleic-acid-binding sites continues to pose a significant challenge. Presently, the predictive efficacy of sequence-bas...
Neural Networks, Computer Language Proteins DNA RNA Binding Sites
View on PubMed DOI

DeepSTF: predicting transcription factor binding sites by interpretable deep neural networks combining sequence and shape.

Briefings in bioinformatics Jul 20, 2023
Precise targeting of transcription factor binding sites (TFBSs) is essential to comprehending transcriptional regulatory processes and investigating cellular function. Although several deep learning algorithms have been created to predict TFBSs, the ...
Neural Networks, Computer DNA Protein Binding Binding Sites Transcription Factors
View on PubMed DOI

GeoBind: segmentation of nucleic acid binding interface on protein surface with geometric deep learning.

Nucleic acids research Jun 9, 2023
Unveiling the nucleic acid binding sites of a protein helps reveal its regulatory functions in vivo. Current methods encode protein sites from the handcrafted features of their local neighbors and recognize them via a classification, which are limite...
Algorithms Nucleic Acids Deep Learning Binding Sites Membrane Proteins
View on PubMed DOI

Identification of metal ion-binding sites in RNA structures using deep learning method.

Briefings in bioinformatics Mar 19, 2023
Metal ion is an indispensable factor for the proper folding, structural stability and functioning of RNA molecules. However, it is very difficult for experimental methods to detect them in RNAs. With the increase of experimentally resolved RNA struct...
Ions Metals Neural Networks, Computer Binding Sites RNA Deep Learning
View on PubMed DOI

Cooperation of local features and global representations by a dual-branch network for transcription factor binding sites prediction.

Briefings in bioinformatics Mar 19, 2023
Interactions between DNA and transcription factors (TFs) play an essential role in understanding transcriptional regulation mechanisms and gene expression. Due to the large accumulation of training data and low expense, deep learning methods have sho...
Binding Sites Transcription Factors DNA Neural Networks, Computer Protein Binding
View on PubMed DOI
Popular Topics
Recent Journals