BACKGROUND: Accurately identifying drug-target interaction (DTI), affinity (DTA), and binding sites (DTS) is crucial for drug screening, repositioning, and design, as well as for understanding the functions of target. Although there are a few online ...
Bromodomain 4 and 9 (BRD4 and BRD9) have been regarded as important targets of drug designs in regard to the treatment of multiple diseases. In our current study, molecular dynamics (MD) simulations, deep learning (DL) and binding free energy calcula...
The physical interactions between proteins are largely determined by the structural properties at their binding interfaces. It was found that the binding interfaces in distinctive protein complexes are highly similar. The structural properties underl...
Journal of molecular graphics & modelling
Apr 17, 2024
This study delves into the prediction of protein-peptide interactions using advanced machine learning techniques, comparing models such as sequence-based, standard CNNs, and traditional classifiers. Leveraging pre-trained language models and multi-vi...
Revealing protein binding sites with other molecules, such as nucleic acids, peptides, or small ligands, sheds light on disease mechanism elucidation and novel drug design. With the explosive growth of proteins in sequence databases, how to accuratel...
Journal of chemical theory and computation
Apr 11, 2024
The Protein Structure Transformer (PeSTo), a geometric transformer, has exhibited exceptional performance in predicting protein-protein binding interfaces and distinguishing interfaces with nucleic acids, lipids, small molecules, and ions. In this st...
Circular RNAs (circRNAs) have surfaced as important non-coding RNA molecules in biology. Understanding interactions between circRNAs and RNA-binding proteins (RBPs) is crucial in circRNA research. Existing prediction models suffer from limited availa...
Protein-DNA and protein-RNA interactions are involved in many biological processes and regulate many cellular functions. Moreover, they are related to many human diseases. To understand the molecular mechanism of protein-DNA binding and protein-RNA b...
Interdisciplinary sciences, computational life sciences
Feb 21, 2024
Circular RNAs (circRNAs) are non-coding RNAs generated by reverse splicing. They are involved in biological process and human diseases by interacting with specific RNA-binding proteins (RBPs). Due to traditional biological experiments being costly, c...
International journal of biological macromolecules
Feb 15, 2024
Magnesium ions (Mg) are essential for the folding, functional expression, and structural stability of RNA molecules. However, predicting Mg-binding sites in RNA molecules based solely on RNA structures is still challenging. The molecular surface, cha...