The recently reported machine learning- or deep learning-based scoring functions (SFs) have shown exciting performance in predicting protein-ligand binding affinities with fruitful application prospects. However, the differentiation between highly si...
Identification of RNA-small molecule binding sites plays an essential role in RNA-targeted drug discovery and development. These small molecules are expected to be leading compounds to guide the development of new types of RNA-targeted therapeutics c...
Technology and health care : official journal of the European Society for Engineering and Medicine
Jan 1, 2023
BACKGROUND: Protein-ligand binding affinity is of significant importance in structure-based drug design. Recently, the development of machine learning techniques has provided an efficient and accurate way to predict binding affinity. However, the pre...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2023
Deep neural networks have demonstrated improved performance at predicting sequence specificities of DNA- and RNA-binding proteins. However, it remains unclear why they perform better than previous methods that rely on k-mers and position weight matri...
Protein science : a publication of the Protein Society
Dec 1, 2022
Knowledge of protein-ligand interactions is beneficial for biological process analysis and drug design. Given the complexity of the interactions and the inadequacy of experimental data, accurate ligand binding residue and pocket prediction remains ch...
Human leukocyte antigens (HLA) regulate various innate and adaptive immune responses and play a crucial immunomodulatory role. Recent studies revealed that non-classical HLA-(HLA-E & HLA-G) based immunotherapies have many advantages over traditional ...
We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predi...
In this study, we introduce an interpretable graph-based deep learning prediction model, AttentionSiteDTI, which utilizes protein binding sites along with a self-attention mechanism to address the problem of drug-target interaction prediction. Our pr...
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...
SUMMARY: Identifying the protein-peptide binding residues is fundamentally important to understand the mechanisms of protein functions and explore drug discovery. Although several computational methods have been developed, most of them highly rely on...
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