We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs. Our method is based on manifold alignment, using LR pairs as inter-data corre...
Journal of molecular graphics & modelling
Feb 11, 2023
Results of the recent Critical Assessment of Protein Structure (CASP) competitions demonstrate that protein backbones can be predicted with very high accuracy. In particular, the artificial intelligence methods of AlphaFold 2 from DeepMind were able ...
In recent years, thanks to advances in computer hardware and dataset availability, data-driven approaches (like machine learning) have become one of the essential parts of the drug design framework to accelerate drug discovery procedures. Constructin...
G-protein-coupled receptor (GPCR) density at the cell surface is thought to regulate receptor function. Spatially resolved measurements of local-density effects on GPCRs are needed but technically limited by density heterogeneity and mobility of memb...
Journal of chemical information and modeling
Jan 16, 2023
Molecular descriptors are essential to quantitative structure activity/property relationship (QSAR/QSPR) models and machine learning models. Here we propose persistent path-spectral (PPS), PPS-based molecular descriptors, and PPS-based machine learni...
Elucidating protein-ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein-ligand interaction is traditionally tackled by molecular docking a...
Protein-protein interactions play a ubiquitous role in biological function. Knowledge of the three-dimensional (3D) structures of the complexes they form is essential for understanding the structural basis of those interactions and how they orchestra...
Developing molecular generative models for directly generating 3D conformation has recently become a hot research area. Here, an autoencoder based generative model was proposed for molecular conformation generation. A unique feature of our method is ...
Antimicrobial peptides (AMPs) are short peptides with a broad spectrum of antimicrobial activity. They play a key role in the host innate immunity of many organisms. The growing threat of microorganisms resistant to antimicrobial agents and the lack ...
Cannabinoid receptors, as part of the family of the G protein-coupled receptors (GPCRs), are involved in various physiological functions. Its subtype cannabinoid receptor subtype 2 (CB2), mainly distributed in the periphery, is a crucial therapeutic ...