IEEE/ACM transactions on computational biology and bioinformatics
Jun 3, 2022
Over the past decade, the demand for automated protein function prediction has increased due to the volume of newly sequenced proteins. In this paper, we address the function prediction task by developing an ensemble system automatically assigning Ge...
IEEE/ACM transactions on computational biology and bioinformatics
Apr 1, 2022
Amphipathic helix (AH)features the segregation of polar and nonpolar residues and plays important roles in many membrane-associated biological processes through interacting with both the lipid and the soluble phases. Although the AH structure has bee...
Journal of chemical information and modeling
Mar 29, 2022
We report for the first time the use of experimental electron density (ED) in the Protein Data Bank for modeling of noncovalent interactions (NCIs) for protein-ligand complexes. Our methodology is based on reduced electron density gradient (RDG) theo...
Journal of computer-aided molecular design
Mar 22, 2022
Modern molecular docking comprises the prediction of pose and affinity. Prediction of docking poses is required for affinity prediction when three-dimensional coordinates of the ligand have not been provided. However, a large number of feature engine...
Drug discovery pipelines typically involve high-throughput screening of large amounts of compounds in a search of potential drugs candidates. As a chemical space of small organic molecules is huge, a "navigation" over it urges for fast and lightweigh...
Understanding the relationship between amino acid sequence and protein function is a long-standing challenge with far-reaching scientific and translational implications. State-of-the-art alignment-based techniques cannot predict function for one-thir...
IEEE/ACM transactions on computational biology and bioinformatics
Feb 3, 2022
Alpha-helical proteins ( αTMPs) are essential in various biological processes. Despite their tertiary structures are crucial for revealing complex functions, experimental structure determination remains challenging and costly. In the past decades, va...
Protein hot spot residues are functional sites in protein-protein interactions. Biological experimental methods are traditionally used to identify hot spot residues, which is laborious and time-consuming. Thus a variety of computational methods were ...
Short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms lie within 2.7 Å, exhibit prominent quantum mechanical characters and are connected to a wide range of essential biomolecular processes. However, exact determination of the geometry an...
Current opinion in structural biology
Dec 23, 2021
Proteins interact through their interfaces to fulfill essential functions in the cell. They bind to their partners in a highly specific manner and form complexes that have a profound effect on understanding the biological pathways they are involved i...