AIMC Topic: Membrane Proteins
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PortPred: Exploiting deep learning embeddings of amino acid sequences for the identification of transporter proteins and their substrates.
Journal of cellular biochemistry
Oct 25, 2023
The physiology of every living cell is regulated at some level by transporter proteins which constitute a relevant portion of membrane-bound proteins and are involved in the movement of ions, small and macromolecules across bio-membranes. The importa...
Integrating Pre-Trained protein language model and multiple window scanning deep learning networks for accurate identification of secondary active transporters in membrane proteins.
Methods (San Diego, Calif.)
Oct 21, 2023
Secondary active transporters play pivotal roles in regulating ion and molecule transport across cell membranes, with implications in diseases like cancer. However, studying transporters via biochemical experiments poses challenges. We propose an eff...
Exploring the World of Membrane Proteins: Techniques and Methods for Understanding Structure, Function, and Dynamics.
Molecules (Basel, Switzerland)
Oct 19, 2023
In eukaryotic cells, membrane proteins play a crucial role. They fall into three categories: intrinsic proteins, extrinsic proteins, and proteins that are essential to the human genome (30% of which is devoted to encoding them). Hydrophobic interacti...
Disclosing the locale of transmembrane proteins within cellular alcove by machine learning approach: systematic review and meta analysis.
Journal of biomolecular structure & dynamics
Sep 28, 2023
Protein subcellular localization is a promising research question in Proteomics and associated fields, including Biological Sciences, Biomedical Engineering, Computational Biology, Bioinformatics, Proteomics, Artificial Intelligence, and Biophysics. ...
Efficient Generation of Paired Single-Cell Multiomics Profiles by Deep Learning.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Apr 28, 2023
Recent advances in single-cell sequencing technology have made it possible to measure multiple paired omics simultaneously in a single cell such as cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) and single-nucleus chromatin...
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...
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