Emilia Lubecka - Publications - Bridge of Knowledge

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Year 2024
Year 2023
Year 2022
  • A coarse‐grained approach to NMR ‐data‐assisted modeling of protein structures
    Publication

    The ESCASA algorithm for analytical estimation of proton positions from coarse-grained geometry developed in our recent work has been implemented in modeling protein structures with the highly coarse-grained UNRES model of polypeptide chains (two sites per residue) and nuclear magnetic resonance (NMR) data. A penalty function with the shape of intersecting gorges was applied to treat ambiguous distance restraints, which automatically...

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  • Early Stages of RNA-Mediated Conversion of Human Prions
    Publication

    - JOURNAL OF PHYSICAL CHEMISTRY B - Year 2022

    Prion diseases are characterized by the conversion of prion proteins from a PrPC fold into a disease-causing PrPSC form that is self-replicating. A possible agent to trigger this conversion is polyadenosine RNA, but both mechanism and pathways of the conversion are poorly understood. Using coarse-grained molecular dynamic simulations we study the time evolution of PrPC over 600 μs. We find that both the D178N mutation and interacting...

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  • Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
    Publication

    - Frontiers in Molecular Biosciences - Year 2022

    In this paper we report the improvements and extensions of the UNRES server (https://unres-server.chem.ug.edu.pl) for physics-based simulations with the coarse-grained UNRES model of polypeptide chains. The improvements include the replacement of the old code with the recently optimized one and adding the recent scale-consistent variant of the UNRES force field, which performs better in the modeling of proteins with the β and the...

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  • Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
    Publication
    • A. K. Sieradzan
    • C. Czaplewski
    • P. Krupa
    • M. Mozolewska
    • A. S. Karczyńska
    • A. G. Lipska
    • E. Lubecka
    • E. Gołaś
    • T. Wirecki
    • M. Makowski... and 2 others

    - Year 2022

    The physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics...

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Year 2021
  • ESCASA : Analytical estimation of atomic coordinates from coarse‐grained geometry for nuclear‐magnetic‐resonance ‐assisted protein structure modeling. I. Backbone and Hβ protons
    Publication

    A method for the estimation of coordinates of atoms in proteins from coarse-grained geometry by simple analytical formulas (ESCASA), for use in nuclear-magnetic-resonance (NMR) data-assisted coarse-grained simulations of proteins is proposed. In this paper, the formulas for the backbone Hα and amide (HN) protons, and the side-chain Hβ protons, given the Cα-trace, have been derived and parameterized, by using the interproton distances...

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  • Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
    Publication
    • A. Antoniak
    • I. Biskupek
    • K. K. Bojarski
    • C. Czaplewski
    • A. Giełdoń
    • M. Kogut
    • M. M. Kogut
    • P. Krupa
    • A. Lipska
    • A. Liwo... and 9 others

    - JOURNAL OF MOLECULAR GRAPHICS & MODELLING - Year 2021

    The UNited RESidue (UNRES) force field was tested in the 14th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP14), in which larger oligomeric and multimeric targets were present compared to previous editions. Three prediction modes were tested (i) ab initio (the UNRES group), (ii) contact-assisted (the UNRES- contact group), and (iii) template-assisted (the UNRES-template...

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  • Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
    Publication
    • A. Kryshtafovych
    • J. Moult
    • W. M. Billings
    • D. Della Corte
    • K. Fidelis
    • S. Kwon
    • K. Olechnovič
    • C. Seok
    • Č. Venclovas
    • J. Won... and 79 others

    - PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS - Year 2021

    Critical Assessment of Structure Prediction (CASP) is an organization aimed at advancing the state of the art in computing protein structure from sequence. In the spring of 2020, CASP launched a community project to compute the structures of the most structurally challenging proteins coded for in the SARS-CoV-2 genome. Forty-seven research groups submitted over 3000 three-dimensional models and 700 sets of accuracy estimates on...

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  • Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
    Publication
    • A. Liwo
    • A. K. Sieradzan
    • A. S. Karczyńska
    • E. Lubecka
    • S. A. Samsonov
    • C. Czaplewski
    • P. Krupa
    • M. Mozolewska

    - Year 2021

    Coarse-grained approaches, in which groups of atoms are represented by single interaction sites, are very important in biological and materials sciences because they enable us to cover the size- and time-scales by several orders of magnitude larger than those available all-atom simulations, while largely keeping the details of the systems studied. The coarse-grained approaches differ by the scheme of reduction and by the origin...

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  • Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment
    Publication
    • M. F. Lensink
    • G. Brysbaert
    • T. Mauri
    • N. Nadzirin
    • S. Velankar
    • R. A. G. Chaleil
    • T. Clarence
    • P. A. Bates
    • R. Kong
    • B. Liu... and 98 others

    - PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS - Year 2021

    We present the results for CAPRI Round 50, the 4th joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 12 targets, including 6 dimers, 3 trimers, and 3 higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly...

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  • Recent Developments in Data-Assisted Modeling of Flexible Proteins
    Publication
    • C. Czaplewski
    • Z. Gong
    • E. Lubecka
    • K. Xue
    • C. Tang
    • A. Liwo

    - Frontiers in Molecular Biosciences - Year 2021

    Many proteins can fold into well-defined conformations. However, intrinsically-disordered proteins (IDPs) do not possess a defined structure. Moreover, folded multi-domain proteins often digress into alternative conformations. Collectively, the conformational dynamics enables these proteins to fulfill specific functions. Thus, most experimental observables are averaged over the conformations that constitute an ensemble. In this...

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