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Rok 2024
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Rok 2022
  • DNAffinity: a machine-learning approach to predict DNA binding affinities of transcription factors
    Publikacja
    • S. Barissi
    • A. Sala
    • M. Wieczór
    • F. Battistini
    • M. Orozco

    - NUCLEIC ACIDS RESEARCH - Rok 2022

    We present a physics-based machine learning approach to predict in vitro transcription factor binding affinities from structural and mechanical DNA properties directly derived from atomistic molecular dynamics simulations. The method is able to predict affinities obtained with techniques as different as uPBM, gcPBM and HT-SELEX with an excellent performance, much better than existing algorithms. Due to its nature, the method can...

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  • Mechanism of reaction of RNA-dependent RNA polymerase from SARS-CoV-2
    Publikacja
    • J. Aranda
    • M. Wieczór
    • M. Terrazas
    • I. Brun-Heath
    • M. Orozco

    - Chem Catalysis - Rok 2022

    We combine molecular dynamics, statistical mechanics, and hybrid quantum mechanics/molecular mechanics simulations to describe mechanistically the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp). Our study analyzes the binding mode of both natural triphosphate substrates as well as remdesivir triphosphate (the active form of drug), which is bound preferentially over ATP by RdRp while...

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Rok 2021
Rok 2020
Rok 2019
Rok 2018
Rok 2017
Rok 2016
Rok 2015
Rok 2014
  • A first-principles study of electron attachment to the fully hydrated bromonucleobases
    Publikacja

    - CHEMICAL PHYSICS LETTERS - Rok 2014

    Degradation mechanism of four brominated nucleobases (BrX), potential DNA radiosensitizers, is studied in explicit water solution, using ab initio molecular dynamics. Several fs long dynamics is needed to localize an electron on the nucleobase. Produced by electron attachment BrX anion radical degrades through the bromide anion abstraction, barrier-free (purines) or with low barrier (pyrimidines), to a reactive nucleobase radical....

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  • Molecular Recognition in Complexes of TRF Proteins with Telomeric DNA
    Publikacja

    Telomeres are specialized nucleoprotein assemblies that protect the ends of linear chromosomes. In humans and many other species, telomeres consist of tandem TTAGGG repeats bound by a protein complex known as shelterin that remodels telomeric DNA into a protective loop structure and regulates telomere homeostasis. Shelterin recognizes telomeric repeats through its two major components known as Telomere Repeat-Binding Factors, TRF1...

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Rok 2012

wyświetlono 2388 razy