AIMC Topic: Membrane Proteins
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Targeting Protein-Protein Interfaces with Peptides: The Contribution of Chemical Combinatorial Peptide Library Approaches.
International journal of molecular sciences
Apr 25, 2023
Protein-protein interfaces play fundamental roles in the molecular mechanisms underlying pathophysiological pathways and are important targets for the design of compounds of therapeutic interest. However, the identification of binding sites on protei...
Higher-order structure formation using refined monomer structures of lipid raft markers, Stomatin, Prohibitin, Flotillin, and HflK/C-related proteins.
FEBS open bio
Mar 17, 2023
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...
Prediction of hydrophilic and hydrophobic hydration structure of protein by neural network optimized using experimental data.
Scientific reports
Feb 7, 2023
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...
Deep learning-driven insights into super protein complexes for outer membrane protein biogenesis in bacteria.
eLife
Dec 28, 2022
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...
DENVIS: Scalable and High-Throughput Virtual Screening Using Graph Neural Networks with Atomic and Surface Protein Pocket Features.
Journal of chemical information and modeling
Sep 26, 2022
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...
MemBrain: A deep learning-aided pipeline for detection of membrane proteins in Cryo-electron tomograms.
Computer methods and programs in biomedicine
Jul 1, 2022
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....
SE-BLTCNN: A channel attention adapted deep learning model based on PSSM for membrane protein classification.
Computational biology and chemistry
Apr 6, 2022
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...
MFPS_CNN: Multi-filter Pattern Scanning from Position-specific Scoring Matrix with Convolutional Neural Network for Efficient Prediction of Ion Transporters.
Molecular informatics
Apr 5, 2022
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 ...
Ab-Initio Membrane Protein Amphipathic Helix Structure Prediction Using Deep Neural Networks.
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...
iTTCA-MFF: identifying tumor T cell antigens based on multiple feature fusion.
Immunogenetics
Mar 5, 2022
Cancer is a terrible disease, recent studies reported that tumor T cell antigens (TTCAs) may play a promising role in cancer treatment. Since experimental methods are still expensive and time-consuming, it is highly desirable to develop automatic com...
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