Membrane proteins (MPs) play an essential role in a broad range of cellular functions, serving as transporters, enzymes, receptors, and communicators, and about ~60% of membrane proteins are primarily used as drug targets. These proteins adopt either...
Membrane protein classification is a key to inferring the function of uncharacterized membrane protein. To get around the time-consuming and expensive biochemical experiments in the wet lab, there has been a lot of research focusing on developing fas...
In cellular transportation mechanisms, the movement of ions across the cell membrane and its proper control are important for cells, especially for life processes. Ion transporters/pumps and ion channel proteins work as border guards controlling the ...
Computer methods and programs in biomedicine
35858496
BACKGROUND AND OBJECTIVE: Cryo-electron tomography (cryo-ET) is an imaging technique that enables 3D visualization of the native cellular environment at sub-nanometer resolution, providing unpreceded insights into the molecular organization of cells....
Recent advances in protein structural modelling have enabled the accurate prediction of the holo 3D structures of almost any protein, however protein function is intrinsically linked to the interactions it makes. While a number of computational appro...
Journal of chemical information and modeling
36154119
Computational methods for virtual screening can dramatically accelerate early-stage drug discovery by identifying potential hits for a specified target. Docking algorithms traditionally use physics-based simulations to address this challenge by estim...
To reach their final destinations, outer membrane proteins (OMPs) of gram-negative bacteria undertake an eventful journey beginning in the cytosol. Multiple molecular machines, chaperones, proteases, and other enzymes facilitate the translocation and...
The hydration structures of proteins, which are necessary for their folding, stability, and functions, were visualized using X-ray and neutron crystallography and transmission electron microscopy. However, complete visualization of hydration structur...
Currently, information on the higher-order structure of Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH)-domain proteins is limited. Briefly, the coordinate information (Refined PH1511.pdb) of the stomatin ortholog, PH1511 monomer, was obtained usi...
Unveiling the nucleic acid binding sites of a protein helps reveal its regulatory functions in vivo. Current methods encode protein sites from the handcrafted features of their local neighbors and recognize them via a classification, which are limite...