Concept
Séquençage des protéines
Publications associées (82)
Development of tools and methods for protein identification: From single molecules to in vivo applications.
As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...
EPFL2024Supplementary dataset for Enzyme promiscuous profiles for protein sequence and reaction annotation
Vassily Hatzimanikatis, Ljubisa Miskovic, Homa Mohammadi Peyhani, Anastasia Sveshnikova
The data and scripts used to produce, analyze, and visualize the results of the manuscript Enzyme promiscuous profiles for protein sequence and reaction annotation by Homa MohammadiPeyhani, Anastasia Sveshnikova, Ljubisa Miskovic, and Vassily Hatzimanikati ...
Zenodo2023Multienzyme deep learning models improve peptide de novo sequencing by mass spectrometry proteomics
Author summaryIn recent years, the application of deep learning represented a breakthrough in the mass spectrometry (MS) field by improving the assignment of the correct sequence of amino acids from observable MS spectra without prior knowledge, also known ...
PUBLIC LIBRARY SCIENCE2023Impact of phylogeny on structural contact inference from protein sequence data
Anne-Florence Raphaëlle Bitbol, Nicola Dietler, Umberto Lupo
Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...
ROYAL SOC2023A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer
Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...
EPFL2023Generative power of a protein language model trained on multiple sequence alignments
Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa, Umberto Lupo
Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...
eLIFE SCIENCES PUBL LTD2023Controlling the immobilization process of an optically enhanced protein microarray for highly reproducible immunoassay
By virtue of its high throughput multiplex detection capability, superior read-out sensitivity, and tiny analyte consumption, an optically enhanced protein microarray assay has been developed as a promising diagnostic tool for various applications, ranging ...
ROYAL SOC CHEMISTRY2021Ultraviolet Photodissociation of Peptides: New Insight on the Mobile Proton Model
Aleksandr Pereverzev, Elizaveta Solovyeva
In this work, we study the mechanism of peptide photodissociation by ultraviolet irradiation at 193 nm wavelength and discuss the role of ionization proton in this process. We found that substituting the ionization proton for the alkali metal cations (sodi ...
PLEIADES PUBLISHING INC2020Method for Identification of Threonine Isoforms in Peptides by Ultraviolet Photofragmentation of Cold Ions
Vladimir Kopysov, Aleksandr Pereverzev, Elizaveta Solovyeva
Identification of isomeric amino acid residues in peptides and proteins is challenging but often highly desired in proteomics. One of the practically important cases that require isomeric assignments is that associated with single-nucleotide polymorphism s ...
AMER CHEMICAL SOC2019Evaluating the similarity of biochemical reactions and its uses for mapping novel and orphan reactions to protein sequences
Recent advances in synthetic biochemistry have resulted in a wealth of de novo hypothetical enzymatic reactions that are not matched to protein-encoding genes, deeming them “orphan”. Nearly half of known metabolic enzymes are also orphan, leaving important ...
2018