Search results for: PROTEIN EMBEDDING - Bridge of Knowledge

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Search results for: PROTEIN EMBEDDING

  • Silica In Silico: A Molecular Dynamics Characterization of the Early Stages of Protein Embedding for Atom Probe Tomography

    Publication
    • G. Novi Inverardi
    • F. Carnovale
    • L. Petrolli
    • S. Taioli
    • G. Lattanzi

    - BIOPHYSICAL JOURNAL - Year 2023

    A novel procedure for the application of atom probe tomography (APT) to the structural analysis of biological systems, has been recently proposed, whereby the specimen is embedded by a silica matrix and ablated by a pulsed laser source. Such a technique, requires that the silica primer be properly inert and bio-compatible, keeping the native structural features of the system at hand, while condensing into an amorphous, glass-like...

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  • t-SNE Highlights Phylogenetic and Temporal Patterns of SARS-CoV-2 Spike and Nucleocapsid Protein Evolution

    Publication
    • G. Tamazian
    • A. Komissarov
    • D. Kobak
    • D. Polyakov
    • E. Andronov
    • S. Nechaev
    • S. Kryzhevich
    • Y. Porozov
    • E. Stepanov

    - Year 2022

    We propose applying t-distributed stochastic neighbor embedding to protein sequences of SARS-CoV-2 to construct, visualize and study the evolutionary space of the coronavirus. The basic idea is to explore the COVID-19 evolution space by using modern manifold learning techniques applied to evolutionary distances between variants. Evolutionary distances have been calculated based on the structures of the nucleocapsid and spike proteins.

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