Physical chemistry chemical physics : PCCP
Mar 8, 2023
The prediction of the free energy (Δ) of binding for protein-protein complexes is of general scientific interest as it has a variety of applications in the fields of molecular and chemical biology, materials science, and biotechnology. Despite its ce...
RNA-protein complexes underlie numerous cellular processes, including basic translation and gene regulation. The high-resolution structure determination of the RNA-protein complexes is essential for elucidating their functions. Therefore, computation...
The journal of physical chemistry letters
Feb 16, 2023
Predicting protein-ligand binding affinities (PLAs) is a core problem in drug discovery. Recent advances have shown great potential in applying machine learning (ML) for PLA prediction. However, most of them omit the 3D structures of complexes and ph...
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 this issue of PLOS Biology, Ibrahim and colleagues demonstrate how AlphaFold-multimer, an artificial intelligence-based structure prediction tool, can be used to identify sequence motifs binding to the ATG8 family of proteins central to autophagy.
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...
Protein-protein interactions (PPIs) govern cellular pathways and processes, by significantly influencing the functional expression of proteins. Therefore, accurate identification of protein-protein interaction binding sites has become a key step in t...
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...
Treatment of COVID-19 with a soluble version of ACE2 that binds to SARS-CoV-2 virions before they enter host cells is a promising approach, however it needs to be optimized and adapted to emerging viral variants. The computational workflow presented ...
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...