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Information of the project and the call

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Coarse-grain modeling of biochemical processes with proteins taking into account water and lipid molecules.

2017/27/B/ST4/00926

Keywords:

coarse-grain force field UNRES expicite water and lipids

Descriptors:

  • ST4_15: Colloid chemistry
  • ST4_13: Solid-state chemistry, surface physicochemistry

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):

dr Adam Sieradzan 

Number of co-investigators in the project: 4

Call: OPUS 14 - announced on 2017-09-15

Amount awarded: 570 200 PLN

Project start date (Y-m-d): 2018-07-13

Project end date (Y-m-d): 2023-07-12

Project duration:: 60 months (the same as in the proposal)

Project status: Project settled

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.

Equipment purchased [PL]

  1. Dwa komputerów.
  2. Nod obliczeniowy (2 szt.) (34 000 PLN)

Information in the final report

  • Publication in academic press/journals (14)
  • Book publications / chapters in book publications (3)
  1. Investigation of Phosphorylation-Induced Folding of an IntrinsicallyDisordered Protein by Coarse-Grained Molecular Dynamics
    Authors:
    Adam K. Sieradzan, Anatolii Korneev, Alexander Begun, Khatuna Kachlishvili, Harold A. Scheraga, Alexander Molochkov, Patrick Senet, Antti J. Niemi, and Gia G. Maisuradze
    Academic press:
    J. Chem. Theory Comput. (rok: 2021, tom: 17, strony: 3203-3220), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jctc.1c00155 - link to the publication
  2. On the need to introduce environmental characteristics in ab initio protein structure prediction using a coarse-grained UNRES force field
    Authors:
    Irena Roterman, Adam Sieradzan, Katarzyna Stapor, Piotr Fabian, Patryk Wesołowski, Leszek Konieczny
    Academic press:
    Journal of Molecular Graphics and Modelling (rok: 2022, tom: 114, strony: 108166), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2022.108166 - link to the publication
  3. The N-Terminal Proline Hinge Motif Controls the Structure of Bovine Herpesvirus 1-Encoded Inhibitor of the Transporter Associated with Antigen Processing Required for its Immunomodulatory Function
    Authors:
    Małgorzata Graul, Natalia Karska, Magda Wąchalska, Paweł Krupa, Magdalena J. Ślusarz, Krystyna Bieńkowska-Szewczyk, Sylwia Rodziewicz-Motowidło, Adam K. Sieradzan*, Andrea D. Lipińska*
    Academic press:
    Journal of Molecular Biology (rok: 2023, tom: 435, strony: 167964), Wydawca: ScienceDirect
    Status:
    Published
    DOI:
    10.1016/j.jmb.2023.167964 - link to the publication
  4. Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin
    Authors:
    Annemarie Danielsson, Sergey A. Samsonov, Adam Liwo, and Adam K. Sieradzan
    Academic press:
    J. Chem. Theory Comput. (rok: 2023, tom: 19, strony: 6023-6036), Wydawca: ACS Publications
    Status:
    Accepted for publication
    DOI:
    10.1021/acs.jctc.3c00511 - link to the publication
  5. Assessment of chemical-crosslink-assisted protein structure modeling in CASP13
    Authors:
    J. Eduardo Fajardo Rojan Shrestha Nelson Gil Adam Belsom Silvia N. Crivelli Cezary Czaplewski Krzysztof Fidelis Sergei Grudinin Mikhail Karasikov Agnieszka S. Karczyńska Andriy Kryshtafovych Alexander Leitner Adam Liwo Emilia A. Lubecka Bohdan Monastyrskyy Guillaume Pagès Juri Rappsilber Adam K. Sieradzan Celina Sikorska Esben Trabjerg Andras Fiser
    Academic press:
    PROTEINS: Structure, Function, and Bioinformatics (rok: 2019, tom: 87, strony: 1283-1297), Wydawca: Wiley Online Library
    Status:
    Published
    DOI:
    10.1002/prot.25816 - link to the publication
  6. Energy landscapes for proteins described by the UNRES coarse-grained potential
    Authors:
    Patryk A. Wesołowski , Adam K. Sieradzan, Michał J. Winnicki, John W.R. Morgan, David J. Wales
    Academic press:
    Biophysical Chemistry (rok: 2023, tom: 303, strony: 107107), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.bpc.2023.107107 - link to the publication
  7. Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer
    Authors:
    Karolina Ziȩba, Magdalena Ślusarz, Rafał Ślusarz, Adam Liwo, Cezary Czaplewsk, iAdam K. Sieradzan
    Academic press:
    The Journal of Physical Chemistry B (rok: 2019, tom: 123, strony: 7829-7839), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.9b06700 - link to the publication
  8. Long-time scale simulations of virus-like particles from three human-norovirus strains
    Authors:
    Agnieszka G. Lipska , Adam K. Sieradzan, Cezary Czaplewski,Andrea D. Lipinska , Krzysztof M. Ocetkiewicz, Jerzy Proficz, Paweł Czarnul, Henryk Krawczyk, Adam Liwo
    Academic press:
    J. Comput. Chem. (rok: 2023, tom: 44, strony: 1470-1483), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/jcc.27087 - link to the publication
  9. Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
    Authors:
    Anna Antoniak, Iga Biskupek, Krzysztof K. Bojarski, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Małgorzata M. Kogut, Paweł Krupa, Agnieszka G. Lipska, Adam Liwo, Emilia A. Lubecka, Mateusz Marcisz, Martyna Maszota-Zieleniak, Sergey A. Samsonov, Adam K. Sieradzan, Magdalena J. Slusarz, Rafał Slusarz, Patryk A. Wesołowski, Karolina Zięba
    Academic press:
    J Mol. Graph. Model. (rok: 2021, tom: 108, strony: 108008), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2021.108008 - link to the publication
  10. Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins
    Authors:
    Adam K. Sieradzan, Jordi Sans-Duñó, Emilia A. Lubecka, Cezary Czaplewski, Agnieszka G. Lipska, Henryk Leszczyński, Krzysztof M. Ocetkiewicz, Jerzy Proficz, Paweł Czarnul, Henryk Krawczyk, Adam Liwo
    Academic press:
    J. Comput Chem. (rok: 2022, tom: 44, strony: 602-625), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/jcc.27026 - link to the publication
  11. Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems
    Authors:
    Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, Agnieszka G. Lipska, Sergey A. Samsonov and Rajesh K. Murarka
    Academic press:
    biomolecules (rok: 2021, tom: 11, strony: 1347), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom11091347 - link to the publication
  12. Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment
    Authors:
    Emilia A.Lubecka, Agnieszka S.Karczyńska, Agnieszka G.Lipska, Adam K. Sieradzan, Karolina Ziȩba, Celina Sikorska, Urszula Uciechowska, Sergey A.Samsonov, Paweł Krupa, Magdalena A.Mozolewska, Łukasz Golon, Artur Giełdoń, Cezary Czaplewski, Rafał Ślusarz, Magdalena Ślusarz, Silvia N.Crivelli, Adam Liwo
    Academic press:
    Journal of Molecular Graphics and Modelling (rok: 2019, tom: 92, strony: 154-166), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2019.07.013 - link to the publication
  13. Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13
    Authors:
    Agnieszka S. Karczyńska, Karolina Ziȩba, Urszula Uciechowska, Magdalena A. Mozolewska, Paweł Krupa, Emilia A. Lubecka, Agnieszka G. Lipska, Celina Sikorska, Sergey A. Samsonov, Adam K. Sieradzan, Artur Giełdoń, Adam Liwo, Rafał Ślusarz, Magdalena Ślusarz, Jooyoung Lee, Keehyoung Joo, and Cezary Czaplewski
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2020, tom: 60, strony: 1844-1864), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jcim.9b00864 - 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 Academic
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad391 - link to the publication
  1. Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field
    Authors:
    Adam K. Sieradzan, Cezary Czaplewski, Paweł Krupa, Magdalena A. Mozolewska, Agnieszka S. Karczyńska, Agnieszka G. Lipska, Emilia A. Lubecka, Ewa Gołaś, Tomasz Wirecki, Mariusz Makowski, Stanisław Ołdziej & Adam Liwo
    Book:
    Protein Folding (rok: 2021, tom: 2376, strony: 399-416), Wydawca: Springer Link
    Status:
    Published
  2. Chapter Two - Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
    Authors:
    Adam Liwo, Cezary Czaplewski, Adam K. Sieradzan, Emilia A. Lubecka, Agnieszka G. Lipska, Łukasz Golon, Agnieszka Karczyńska, Paweł Krupa, Magdalena A. Mozolewska,, Mariusz Makowski, Robert Ganzynkowicz, Artur Giełdoń, Maciej Maciejczyk
    Book:
    Progress in Molecular Biology and Translational Science (rok: 2020, tom: 170, strony: 73-122), Wydawca: Elsevier
    Status:
    Published
  3. Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry
    Authors:
    Adam Liwo, Adam K. Sieradzan, Agnieszka S. Karczy ́nska, Emilia A. Lubecka, Sergey A. Samsonov, Cezary Czaplewski, Paweł Krupa, and Magdalena Mozolewska
    Book:
    Practical Aspects of Computational Chemistry V (rok: 2022, tom: 1, strony: 31-69), Wydawca: Springer
    Status:
    Published

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