Predicting the various binding sites of a protein from its structure sheds light on its function and paves the way towards design of interaction inhibitors. Here, we report ScanNet, a freely available web server for prediction of protein-protein, pro...
The binding and catalytic functions of proteins are generally mediated by a small number of functional residues held in place by the overall protein structure. Here, we describe deep learning approaches for scaffolding such functional sites without n...
BACKGROUND: The transforming growth factor beta-1 (TGF β-1) cytokine exerts both pro-tumor and anti-tumor effects in carcinogenesis. An increasing body of literature suggests that TGF β-1 signaling outcome is partially dependent on the regulatory tar...
International journal of molecular sciences
Jul 12, 2022
All living organisms require metal ions for their energy production and metabolic and biosynthetic processes. Within cells, the metal ions involved in the formation of adducts interact with metabolites and macromolecules (proteins and nucleic acids)....
Circular RNA (circRNA) can exert biological functions by interacting with RNA-binding protein (RBP), and some deep learning-based methods have been developed to predict RBP binding sites on circRNA. However, most of these methods identify circRNA-RBP...
Protein-protein interactions (PPIs) are responsible for various essential biological processes. This information can help develop a new drug against diseases. Various experimental methods have been employed for this purpose; however, their applicatio...
European journal of medicinal chemistry
Jul 1, 2022
Artificial intelligence (AI) has been recognized as a powerful technique that can accelerate drug discovery during the hit compound identification step. However, most simple deep learning models have been used for naive pre-filtering as the predictio...
BACKGROUND: Addressing the laborious nature of traditional biological experiments by using an efficient computational approach to analyze RNA-binding proteins (RBPs) binding sites has always been a challenging task. RBPs play a vital role in post-tra...
BACKGROUND: Several computational advances have been achieved in the drug discovery field, promoting the identification of novel drug-target interactions and new leads. However, most of these methodologies have been overlooking the importance of prov...
Optimization of gene expression levels is an essential part of the organism design process. Fine control of this process can be achieved by engineering transcription and translation control elements, including the ribosome binding site (RBS). Unfortu...