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Protein Binding

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KDeep: a new memory-efficient data extraction method for accurately predicting DNA/RNA transcription factor binding sites.

Journal of translational medicine Oct 16, 2023
This paper addresses the crucial task of identifying DNA/RNA binding sites, which has implications in drug/vaccine design, protein engineering, and cancer research. Existing methods utilize complex neural network structures, diverse input types, and ...
DNA Binding Sites Transcription Factors Neural Networks, Computer Protein Binding
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Epigenetic target identification strategy based on multi-feature learning.

Journal of biomolecular structure & dynamics Oct 12, 2023
The identification of potential epigenetic targets for a known bioactive compound is essential and promising as more and more epigenetic drugs are used in cancer clinical treatment and the availability of chemogenomic data related to epigenetics incr...
Protein Binding Epigenesis, Genetic Molecular Docking Simulation Drug Discovery Epigenomics Ligands Humans Neural Networks, Computer Machine Learning Algorithms
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ResBiGAAT: Residual Bi-GRU with attention for protein-ligand binding affinity prediction.

Computational biology and chemistry Oct 11, 2023
Protein-ligand interaction plays a crucial role in drug discovery, facilitating efficient drug development and enabling drug repurposing. Several computational algorithms, such as Graph Neural Networks and Convolutional Neural Networks, have been pro...
Neural Networks, Computer Proteins Algorithms Ligands Deep Learning Protein Binding
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CRBSP:Prediction of CircRNA-RBP Binding Sites Based on Multimodal Intermediate Fusion.

IEEE/ACM transactions on computational biology and bioinformatics Oct 9, 2023
Circular RNA (CircRNA) is widely expressed and has physiological and pathological significance, regulating post-transcriptional processes via its protein-binding activity. However, whereas much work has been done on linear RNA and RNA binding protein...
Binding Sites Protein Binding Neural Networks, Computer RNA RNA, Circular
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RefinePocket: An Attention-Enhanced and Mask-Guided Deep Learning Approach for Protein Binding Site Prediction.

IEEE/ACM transactions on computational biology and bioinformatics Oct 9, 2023
Protein binding site prediction is an important prerequisite task of drug discovery and design. While binding sites are very small, irregular and varied in shape, making the prediction very challenging. Standard 3D U-Net has been adopted to predict b...
Drug Discovery Deep Learning Binding Sites Protein Binding Image Processing, Computer-Assisted Protein Domains
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WVDL: Weighted Voting Deep Learning Model for Predicting RNA-Protein Binding Sites.

IEEE/ACM transactions on computational biology and bioinformatics Oct 9, 2023
RNA-binding proteins are important for the process of cell life activities. High-throughput technique experimental method to discover RNA-protein binding sites is time-consuming and expensive. Deep learning is an effective theory for predicting RNA-p...
RNA Deep Learning Protein Binding Binding Sites RNA-Binding Proteins
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Efficient and accurate large library ligand docking with KarmaDock.

Nature computational science Sep 21, 2023
Ligand docking is one of the core technologies in structure-based virtual screening for drug discovery. However, conventional docking tools and existing deep learning tools may suffer from limited performance in terms of speed, pose quality and bindi...
Neural Networks, Computer Molecular Docking Simulation Protein Binding Ligands Proteins
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Improved prediction of protein-protein interactions by a modified strategy using three conventional docking software in combination.

International journal of biological macromolecules Aug 24, 2023
Proteins play a crucial role in many biological processes, where their interaction with other proteins are integral. Abnormal protein-protein interactions (PPIs) have been linked to various diseases including cancer, and thus targeting PPIs holds pro...
Software Neoplasms Protein Binding Humans Artificial Intelligence Proteins Peptides Molecular Docking Simulation
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Deep learning-based method for predicting and classifying the binding affinity of protein-protein complexes.

Biochimica et biophysica acta. Proteins and proteomics Aug 9, 2023
Protein-protein interactions (PPIs) play a critical role in various biological processes. Accurately estimating the binding affinity of PPIs is essential for understanding the underlying molecular recognition mechanisms. In this study, we employed a ...
Protein Binding Deep Learning Proteins
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Deep-learning-enabled protein-protein interaction analysis for prediction of SARS-CoV-2 infectivity and variant evolution.

Nature medicine Jul 31, 2023
Host-pathogen interactions and pathogen evolution are underpinned by protein-protein interactions between viral and host proteins. An understanding of how viral variants affect protein-protein binding is important for predicting viral-host interactio...
Artificial Intelligence Protein Binding SARS-CoV-2 Humans Deep Learning COVID-19
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