Synthetic binding proteins (SBPs) are a class of protein binders that are artificially created and do not exist naturally. Their broad applications in tackling challenges of research, diagnostics, and therapeutics have garnered significant interest. ...
Journal of chemical theory and computation
Jan 3, 2025
The development of machine-learning (ML) potentials offers significant accuracy improvements compared to molecular mechanics (MM) because of the inclusion of quantum-mechanical effects in molecular interactions. However, ML simulations are several ti...
Journal of chemical information and modeling
Dec 26, 2024
In recent years, the deep learning (DL) technique has rapidly developed and shown great success in scoring the protein-ligand binding affinities. The protein-ligand conformation optimization based on DL-derived scoring functions holds broad applicati...
The src-homology 2 domain-containing phosphatase 2 (SHP2) is a human cytoplasmic protein tyrosine phosphatase that plays a crucial role in cellular signal transduction. Aberrant activation and mutations of SHP2 are associated with tumor growth and im...
The interaction between peptides and major histocompatibility complex (MHC) molecules is pivotal in autoimmunity, pathogen recognition and tumor immunity. Recent advances in cancer immunotherapies demand for more accurate computational prediction of ...
The mis-folding and aggregation of intrinsically disordered proteins (IDPs) such as α-synuclein (αS) underlie the pathogenesis of various neurodegenerative disorders. However, targeting αS with small molecules faces challenges due to the lack of defi...
Binding affinity prediction has been considered as a fundamental task in drug discovery. Despite much effort to improve accuracy of binding affinity prediction, the prior work considered only macro-level features that can represent the characteristic...
Journal of chemical information and modeling
Dec 10, 2024
Kinase inhibitors are an important class of anticancer drugs, with 80 inhibitors clinically approved and >100 in active clinical testing. Most bind competitively in the ATP-binding site, leading to challenges with selectivity for a specific kinase, r...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 10, 2024
The prediction of drug-target affinity (DTA) plays a crucial role in drug development and the identification of potential drug targets. In recent years, computer-assisted DTA prediction has emerged as a significant approach in this field. In this stu...
IEEE/ACM transactions on computational biology and bioinformatics
Dec 10, 2024
Graph neural networks have drawn increasing attention and achieved remarkable progress recently due to their potential applications for a large amount of irregular data. It is a natural way to represent protein as a graph. In this work, we focus on p...