Journal of computer-aided molecular design
Dec 20, 2014
The assessment of binding affinity between ligands and the target proteins plays an essential role in drug discovery and design process. As an alternative to widely used scoring approaches, machine learning methods have also been proposed for fast pr...
Proteomics experiments often generate a vast amount of data. However, the simple identification and quantification of proteins from a cell proteome or subproteome is not sufficient for the full understanding of complex mechanisms occurring in the bio...
Bioscience, biotechnology, and biochemistry
Apr 22, 2025
Protein kinase C (PKC) is a family of serine/threonine kinases, and PKC ligands have the potential to be therapeutic seeds for cancer, Alzheimer's disease, and human immunodeficiency virus infection. However, in addition to desired therapeutic effect...
Deep learning (DL) methods have drastically advanced structure-based drug discovery by directly predicting protein structures from sequences. Recently, these methods have become increasingly accurate in predicting complexes formed by multiple protein...
MOTIVATION: Identifying antibody binding sites, is crucial for developing vaccines and therapeutic antibodies, processes that are time-consuming and costly. Accurate prediction of the paratope's binding site can speed up the development by improving ...
BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, trai...
Identifying interactions between drugs and targets is crucial for drug discovery and development. Nevertheless, the determination of drug-target binding affinities (DTAs) through traditional experimental methods is a time-consuming process. Conventio...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
The interactions between long noncoding RNA (lncRNA) and protein play crucial roles in various biological processes. Computational methods are essential for predicting lncRNA-protein interactions and deciphering their mechanisms. In this chapter, we ...
Protein science : a publication of the Protein Society
Jan 1, 2025
Computational methods to predict binding affinity of protein-ligand complex have been used extensively to design inhibitors for proteins selected as drug targets. In recent years machine learning (ML) is being increasingly used for design of drugs/in...
Toxicological sciences : an official journal of the Society of Toxicology
Jan 1, 2025
Per- and polyfluoroalkyl substances (PFAS) are a diverse class of anthropogenic chemicals; many are persistent, bioaccumulative, and mobile in the environment. Worldwide, PFAS bioaccumulation causes serious adverse health impacts, yet the physiochemi...