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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