Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Data-assisted modeling of the ensemble structure of intrinsically disordered proteins and their assemblies

2021/40/Q/ST4/00035

Keywords:

intrinsically disordered proteins protein dynamics coarse-grained modelling nuclear magnetic resonance spectroscopy small-angle X-ray scattering chemical cross-linking mass spectroscopy

Descriptors:

  • ST4_004:
  • ST4_009:
  • ST4_002:

Panel:

ST4 - Chemistry: physical chemistry/chemical physics, theoretical chemistry, analytical chemistry, inorganic chemistry, organic chemistry, method development

Host institution :

Uniwersytet Gdański, Wydział Chemii

woj. pomorskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Józef Adam Liwo 

Number of co-investigators in the project: 8

Call: SHENG 2 - announced on 2020-12-15

Amount awarded: 1 630 572 PLN

Project start date (Y-m-d): 2022-02-01

Project end date (Y-m-d): 2025-09-30

Project duration:: 44 months (the same as in the proposal)

Project status: Pending project

Project description

Download the project description in a pdf file

Note - project descriptions were prepared by the authors of the applications themselves and placed in the system in an unchanged form.

Information in the final report

  • Publication in academic press/journals (17)
  1. Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model
    Authors:
    Iga Biskupek, Cezary Czaplewski, Justyna Sawicka, Emilia Iłowska, Maria Dzierżyńska, Sylwia Rodziewicz-Motowidło, Adam Liwo
    Academic press:
    Biomolecules (rok: 2022, tom: 12, strony: 1140), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom12081140 - link to the publication
  2. Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery
    Authors:
    Celina Sikorska, Adam Liwo
    Academic press:
    Journal of Physical Chemistry B (rok: 2022, tom: 126, strony: 9493−9505), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.2c04610 - link to the publication
  3. Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery
    Authors:
    Celina Sikorska, Adam Liwo
    Academic press:
    Journal of Physical Chemistry B (rok: 2022, tom: 126, strony: 9493−9505), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.2c04610 - link to the publication
  4. Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model
    Authors:
    Iga Biskupek, Cezary Czaplewski, Justyna Sawicka, Emilia Iłowska, Maria Dzierżyńska, Sylwia Rodziewicz-Motowidło, Adam Liwo
    Academic press:
    Biomolecules (rok: 2022, tom: 12, strony: 1140), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom12081140 - link to the publication
  5. Toward Consistent Physics-Based Modeling of Local Backbone Structures and Chirality Change of Proteins in Coarse-Grained Approaches
    Authors:
    Agnieszka G. Lipska, Adam K. Sieradzan, Sümeyye Atmaca, Cezary Czaplewski, and Adam Liwo
    Academic press:
    Journal of Physical Chemistry Letters (rok: 2023, tom: 14, strony: 9824-9833), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jpclett.3c01988 - link to the publication
  6. Long-time scale simulations of virus-like particles from three human-norovirus strains
    Authors:
    Agnieszka G. Lipska, Adam K. Sieradzan, Cezary Czaplewski, Andrea D. Lipińska, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Paweł Czarnul, Henryk Krawczyk, Adam Liwo
    Academic press:
    Journal of Computational Chemistry (rok: 2023, tom: 44, strony: 1470-1483), Wydawca: John Wiley & Sons
    Status:
    Published
    DOI:
    10.1002/jcc.27087 - link to the publication
  7. Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach
    Authors:
    Adam Liwo 1, Maciej Pyrka, Cezary Czaplewski, Xubiao Peng, Antti J. Niemi
    Academic press:
    Biomolecules (rok: 2023, tom: 13, strony: 941), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ - link to the publication
  8. Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
    Authors:
    Rafał Ślusarz, Emilia A. Lubecka, Cezary Czaplewski, Adam Liwo
    Academic press:
    Frontiers in Molecular Biosciences (rok: 2022, tom: 9, strony: 1071428), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fmolb.2022.1071428 - link to the publication
  9. Two-Stage Recognition Mechanism of the SARS-CoV-2 Receptor-Binding Domain to Angiotensin-Converting Enzyme-2 (ACE2)
    Authors:
    Iga Biskupek, Artur Giełdoń
    Academic press:
    International Journal of Molecular Sciences (rok: 2024, tom: 25, strony: 679), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms25010679 - link to the publication
  10. Multi-GPU UNRES for scalable coarse-grained simulations of very large protein systems
    Authors:
    Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Paweł Czarnul
    Academic press:
    Computer Physics Communication (rok: 2024, tom: 298, strony: 109112), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.cpc.2024.109112 - link to the publication
  11. A coarse-grained approach to NMR-data-assisted modeling of protein structures
    Authors:
    Emilia Lubecka, Adam Liwo
    Academic press:
    Journal of Computational Chemistry (rok: 2022, tom: 43, strony: 2047–2059), Wydawca: John Wiley & Sons
    Status:
    Published
    DOI:
    10.1002/jcc.27003 - link to the publication
  12. Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins
    Authors:
    Adam K. Sieradzan, Jordi Sans-Duño, Emilia A. Lubecka, Cezary Czaplewski, Agnieszka G. Lipska, Henryk Leszczyński, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Paweł Czarnul Henryk Krawczyk, Adam Liwo
    Academic press:
    Journal of Computational Chemistry (rok: 2023, tom: 44, strony: 602–625), Wydawca: John Wiley & Sons
    Status:
    Published
    DOI:
    10.1002/jcc.27026 - link to the publication
  13. Assessment of Two Restraint Potentials for Coarse-Grained Chemical-Cross-Link-Assisted Modeling of Protein Structures
    Authors:
    Mateusz Leśniewski, Maciej Pyrka, Cezary Czaplewski, Nguyen Truong Co, Yida Jiang, Zhou Gong, Chun Tang, and Adam Liwo
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2024, tom: 64, strony: 1377-1393), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.3c01890 - link to the publication
  14. UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales
    Authors:
    Krzysztof M. Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka G. Lipska, Adam Liwo, Jerzy Proficz, Adam K. Sieradzan, Paweł Czarnul
    Academic press:
    Bioinformatics (rok: 2023, tom: 39, strony: btad391), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad391 - link to the publication
  15. A coarse-grained approach to NMR-data-assisted modeling of protein structures
    Authors:
    Emilia Lubecka, Adam Liwo
    Academic press:
    Journal of Computational Chemistry (rok: 2022, tom: 43, strony: 2047–2059), Wydawca: John Wiley & Sons
    Status:
    Published
    DOI:
    10.1002/jcc.27003 - link to the publication
  16. Improvements and new functionalities of UNRES server for coarse-grained modeling of protein structure, dynamics, and interactions
    Authors:
    Rafał Ślusarz, Emilia A. Lubecka, Cezary Czaplewski, Adam Liwo
    Academic press:
    Frontiers in Molecular Biosciences (rok: 2022, tom: 9, strony: 1071428), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fmolb.2022.1071428 - link to the publication
  17. Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins
    Authors:
    Adam K. Sieradzan, Jordi Sans-Duño, Emilia A. Lubecka, Cezary Czaplewski, Agnieszka G. Lipska, Henryk Leszczyński, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Paweł Czarnul Henryk Krawczyk, Adam Liwo
    Academic press:
    Journal of Computational Chemistry (rok: 2023, tom: 44, strony: 602–625), Wydawca: John Wiley & Sons
    Status:
    Published
    DOI:
    10.1002/jcc.27026 - link to the publication

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