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An integrated approach to modeling protein structure and dynamics based on the UNRES coarse-grained force field and bioinformatics methods and limited experimental data.

2017/26/M/ST4/00044

Keywords:

protein structure prediction coarse-grained force fields template-based modeling molecular dynamics global optimization methods

Descriptors:

  • ST4_15: Colloid chemistry
  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation
  • NZ1_4: Structural biology

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 hab. Cezary Czaplewski 

Number of co-investigators in the project: 8

Call: HARMONIA 9 - announced on 2017-06-14

Amount awarded: 503 440 PLN

Project start date (Y-m-d): 2018-04-13

Project end date (Y-m-d): 2023-04-12

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.

Information in the final report

  • Publication in academic press/journals (20)
  • Book publications / chapters in book publications (3)
  1. Theoretical Investigation of the Coronavirus SARS-CoV-2 (COVID-19) Infection Mechanism and Selectivity
    Authors:
    Iga Biskupek, Adam Sieradzan, Cezary Czaplewski, Adam Liwo, Adam Lesner, Artur Giełdoń
    Academic press:
    Molecules (rok: 2022, tom: 27, strony: 2080), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ - link to the publication
  2. 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 Zięba, Celina Sikorska, Urszula Uciechowska, Sergey A. Samsonov, Paweł Krupa, Magdalena A. Mozolewska, Łukasz Golon, Artur Giełdoń, Cezary Czaplewski, Rafał Ślusarz b, 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
  3. 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: Wiley
    Status:
    Published
    DOI:
    10.1002/jcc.27087 - link to the publication
  4. Modeling SARS‐CoV‐2 proteins in the CASP‐commons experiment
    Authors:
    Andriy Kryshtafovych, John Moult, Wendy M. Billings, Dennis Della Corte, Krzysztof Fidelis, Sohee Kwon, Kliment Olechnovič, Chaok Seok, Česlovas Venclovas, Jonghun Won, Badri Adhikari, Recep Adiyaman, Joaquim Aguirre-Plans, Minkyung Baek, David Baker, Frederico Baldassarre, Jacob Barger, Sutanu Bhattacharya, Debswapna Bhattacharya, Mor Bitton, Renzhi Cao, Jianlin Cheng, Charles Christoffer, Cezary Czaplewski, Zongyang Du, Arne Elofsson, Eshel Faraggi, Michael Feig, Narcis Fernandez-Fuentes, Nick Grishin, Sergei Grudinin, Zhiye Guo, Yuya Hanazono, Demis Hassabis, Bryce Hedelius, Lim Heo, Cassandra Hunt, Ilia Igashov, Takashi Ishida, Robert L. Jernigan, David Jones, John Jumper, Maria Kadukova, Shaun Kandathil, Chen Keasar, Daisuke Kihara, Lisa Kinch, Yasuomi Kiyota, Andrzej Kloczkowski, Pushmeet Kohli, Mateusz Kogut, Elodie Laine, Cade Lilley, Jian Liu, Józef Adam Liwo, Emilia Lubecka, Arup Mondal, Connor J. Morris, Liam J. McGuffin, Alexis Molina, Tsukasa Nakamura, Baldo Oliva, Alberto Perez, Gabriele Pozzati, Daipayan Sarkar, Rin Sato, Torsten Schwede, Bikash Shrestha, Tomer Sidi, Gabriel Studer, Md Hossain Shuvo, Mayuko Takeda-Shitaka, Yuma Takei, Genki Terashi, Kentaro Tomii, Yuko Tsuchiya, Kathryn Tunyasuvunakool, Björn Wallner, Tianqi Wu, Jinbo Xu, Yu Yamamori, Jianyi Yang, Lisha Ye, Chengxin Zhang, Yang Zhang, Wei Zheng
    Academic press:
    Proteins-Structure Function and Bioinformatics (rok: 2021, tom: 89, strony: 1987-1996), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.26231 - link to the publication
  5. Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment
    Authors:
    Anna Antoniak, Iga Biskupek, Krzysztof Bojarski, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Małgorzata Kogut, Paweł Krupa, Agnieszka Lipska, Józef Adam Liwo, Emilia Lubecka, Mateusz Marcisz, Martyna Maszota-Zieleniak, Sergey Samsonov, Adam Sieradzan, Magdalena Ślusarz, Rafał Ślusarz, Patryk Wesołowski, Karolina Zięba
    Academic press:
    Journal of Molecular Graphics & Modelling (rok: 2021, tom: 108, strony: 108008), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2021.108008 - link to the publication
  6. 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: Wiley
    Status:
    Published
    DOI:
    10.1002/jcc.27026 - link to the publication
  7. Prediction of protein assemblies, the next frontier: the CASP14‐CAPRI experiment
    Authors:
    Marc F. Lensink, Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael A. G. Chaleil, Tereza Clarence, Paul A. Bates, Ren Kong, Bin Liu, Guangbo Yang, Ming Liu, Hang Shi, Xufeng Lu, Shan Chang, Raj S. Roy, Farhan Quadir, Jian Liu, Jianlin Cheng, Anna Antoniak, Cezary Czaplewski, Artur Giełdoń, Mateusz Kogut, Agnieszka Lipska, Józef Adam Liwo, Emilia Lubecka, Martyna Maszota-Zieleniak, Adam Sieradzan, Rafał Ślusarz, Patryk Wesołowski, Karolina Zięba, Carlos A. Del Carpio Muñoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J. Gray, Alexandre M. J. J. Bonvin, Francesco Ambrosetti, Rodrigo Vargas Honorato, Zuzana Jandova, Brian Jiménez‐García, Panagiotis I. Koukos, Siri Van Keulen, Charlotte W. Van Noort, Manon Réau, Jorge Roel‐Touris, Sergei Kotelnikov, Dzmitry Padhorny, Kathryn A. Porter, Andrey Alekseenko, Mikhail Ignatov, Israel Desta, Ryota Ashizawa, Zhuyezi Sun, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A. Rodríguez‐Lumbreras, Juan Fernandez‐Recio, Agnieszka Karczyńska, Sergei Grudinin, Yumeng Yan, Hao Li, Peicong Lin, Sheng‐You Huang, Charles Christoffer, Genki Terashi, Jacob Verburgt, Daipayan Sarkar, Tunde Aderinwale, Xiao Wang, Daisuke Kihara, Tsukasa Nakamura, Yuya Hanazono, Ragul Gowthaman, Johnathan D. Guest, Rui Yin, Ghazaleh Taherzadeh, Brian G. Pierce, Didier Barradas‐Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yuanfei Sun, Shaowen Zhu, Yang Shen, Taeyong Park, Hyeonuk Woo, Jinsol Yang, Sohee Kwon, Jonghun Won, Chaok Seok, Yasuomi Kiyota, Shinpei Kobayashi, Yoshiki Harada, Mayuko Takeda‐Shitaka, Petras J. Kundrotas, Amar Singh, Ilya A. Vakser, Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas, Rui Duan, Liming Qiu, Xianjin Xu, Shuang Zhang, Xiaoqin Zou, Shoshana J. Wodak
    Academic press:
    Proteins-Structure Function and Bioinformatics (rok: 2021, tom: 89, strony: 1800-1823), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.26222 - link to the publication
  8. Blind prediction of homo‐ and hetero‐protein complexes: The CASP13‐CAPRI experiment
    Authors:
    Marc F. Lensink , Guillaume Brysbaert , Nurul Nadzirin , Sameer Velankar , Raphaël A. G. Chaleil , Tereza Gerguri , Paul A. Bates , Elodie Laine , Alessandra Carbone , Sergei Grudinin , Ren Kong , Ran‐Ran Liu , Xi‐Ming Xu , Hang Shi , Shan Chang , Miriam Eisenstein , Agnieszka Karczyńska , Cezary Czaplewski , Emilia Lubecka , Agnieszka Lipska , Paweł Krupa , Magdalena Mozolewska , Łukasz Golon , Sergey Samsonov , Józef Adam Liwo , Silvia N. Crivelli , Guillaume Pagès , Mikhail Karasikov , Maria Kadukova , Yumeng Yan , Sheng‐You Huang , Mireia Rosell , Luis A. Rodríguez‐Lumbreras , Miguel Romero‐Durana , Lucía Díaz‐Bueno , Juan Fernandez‐Recio , Charles Christoffer , Genki Terashi , Woong‐Hee Shin , Tunde Aderinwale , Sai Raghavendra Maddhuri Venkata Subraman , Daisuke Kihara , Dima Kozakov , Sandor Vajda , Kathryn Porter , Dzmitry Padhorny , Israel Desta , Dmitri Beglov , Mikhail Ignatov , Sergey Kotelnikov , Iain H. Moal , David W. Ritchie , Isaure Chauvot de Beauchene , Bernard Maigret , Marie‐Dominique Devignes , Maria E. Ruiz Echartea , Didier Barradas‐Bautista , Zhen Cao , Luigi Cavallo , Romina Oliva , Yue Cao , Yang Shen , Minkyung Baek , Taeyong Park , Hyeonuk Woo , Chaok Seok , Merav Braitbard , Lirane Bitton , Dina Scheidman‐Duhovny , Justas Dapkūnas , Kliment Olechnovič , Česlovas Venclovas , Petras J. Kundrotas , Saveliy Belkin , Devlina Chakravarty , Varsha D. Badal , Ilya A. Vakser , Thom Vreven , Sweta Vangaveti , Tyler Borrman , Zhiping Weng , Johnathan D. Guest , Ragul Gowthaman , Brian G. Pierce , Xianjin Xu , Rui Duan , Liming Qiu , Jie Hou , Benjamin Ryan Merideth , Zhiwei Ma , Jianlin Cheng , Xiaoqin Zou , Panagiotis I. Koukos , Jorge Roel‐Touris , Francesco Ambrosetti , Cunliang Geng , Jörg Schaarschmidt , Mikael E. Trellet , Adrien S. J. Melquiond , Li Xue , Brian Jiménez‐García , Charlotte W. Noort , Rodrigo V. Honorato , Alexandre M. J. J. Bonvin , Shoshana J. Wodak
    Academic press:
    Proteins-Structure Function and Bioinformatics (rok: 2019, tom: 87, strony: 1200-1221), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.25838 - link to the publication
  9. Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins.
    Authors:
    Adam Liwo, Cezary Czaplewski
    Academic press:
    Journal of Chemical Physics (rok: 2020, tom: 152, strony: 54902), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.5138991 - link to the publication
  10. Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models
    Authors:
    Karolina Zięba, Cezary Czaplewski, Józef Adam Liwo, Giuseppe Graziano
    Academic press:
    Physical Chemistry Chemical Physics (rok: 2020, tom: 22, strony: 4758-4771), Wydawca: RSC Publications
    Status:
    Published
    DOI:
    10.1039/C9CP06627F - link to the publication
  11. UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics
    Authors:
    Cezary Czaplewski, Agnieszka Karczyńska, Adam K. Sieradzan, Adam Liwo
    Academic press:
    Nucleic Acids Research (rok: 2018, tom: 46, strony: W304-W309), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gky328 - link to the publication
  12. 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 Karczyńska , Andriy Kryshtafovych , Alexander Leitner , Józef Adam Liwo , Emilia Lubecka , Bohdan Monastyrskyy , Guillaume Pagès , Juri Rappsilber , Adam Sieradzan , Celina Sikorska , Esben Trabjerg , Andras Fiser
    Academic press:
    Proteins-Structure Function and Bioinformatics (rok: 2019, tom: 87, strony: 1283-1297), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.25816 - link to the publication
  13. 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
  14. Pseudopotentials for coarse‐grained cross‐link‐assisted modeling of protein structures
    Authors:
    Mateusz Kogut, Zhou Gong, Chun Tang, Józef Adam Liwo
    Academic press:
    Journal of Computational Chemistry (rok: 2021, tom: 42, strony: 2054-2067), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/jcc.26736 - link to the publication
  15. Recent developments in data-assisted modeling of flexible proteins
    Authors:
    Cezary Czaplewski, Zhou Gong, Emilia Lubecka, Kai Xue, Chun Tang, Józef Adam Liwo
    Academic press:
    Frontiers in Molecular Biosciences (rok: 2021, tom: 8, strony: 765562), Wydawca: Frontiers Media SA
    Status:
    Published
    DOI:
    10.3389/fmolb.2021.765562 - link to the publication
  16. Theory and practice of coarse-grained molecular dynamics of biologically important systems
    Authors:
    Adam Liwo, Cezary Czaplewski, Adam Sieradzan, Agnieszka Lipska, Sergey Samsonov, Rajesh K. Murarka
    Academic press:
    Biomolecules (rok: 2021, tom: 11, strony: 1347), Wydawca: Multidisciplinary Digital Publishing Institute (MDPI)
    Status:
    Published
    DOI:
    10.3390/biom11091347 - link to the publication
  17. UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales
    Authors:
    Krzysztof Ocetkiewicz, Cezary Czaplewski, Henryk Krawczyk, Agnieszka Lipska, Józef Adam Liwo, Jerzy Proficz, Adam Sieradzan, Paweł Czarnul
    Academic press:
    Bioinformatics (rok: 2023, tom: 39, strony: btad391), Wydawca: Oxford Univ Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad391 - link to the publication
  18. Improved consensus-fragment selection in template-assisted prediction of protein structures with the UNRES force field in CASP13
    Authors:
    Agnieszka Karczyńska, Karolina Zięba, Urszula Uciechowska, Magdalena Mozolewska, Paweł Krupa, Emilia Lubecka, Agnieszka Lipska, Celina Sikorska, Sergey Samsonov, Adam Sieradzan, Artur Giełdoń, Adam Liwo, Rafał Ślusarz, Magdalena Ślusarz, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2020, tom: 60, strony: 1844-1864), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.9b00864 - link to the publication
  19. 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 and Adam Liwo
    Academic press:
    Frontiers in Molecular Biosciences (rok: 2022, tom: 9, strony: 1071428), Wydawca: Frontiers Media SA
    Status:
    Published
    DOI:
    10.3389/fmolb.2022.1071428 - link to the publication
  20. Long-Time Dynamics of Selected Molecular-Motor Components Using a Physics-Based Coarse-Grained Approach
    Authors:
    Adam Liwo, 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/biom13060941 - link to the publication
  1. 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 (rok: 2022, tom: V, strony: 31-69), Wydawca: Springer
    Status:
    Published
  2. Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Through Cluster-Cumulant Scope
    Authors:
    Adam Liwo, Adam K. Sieradzan, and Cezary Czaplewski
    Book:
    Protein Supersecondary Structures: Methods and Protocols, Methods in Molecular Biology (rok: 2019, tom: vol. 1958, strony: 133-146), Wydawca: Humana Press
    Status:
    Published
  3. Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers
    Authors:
    Adam Liwo, Cezary Czaplewskia, Adam K. Sieradzan, Emilia A. Lubecka, Agnieszka G. Lipska, Łukasz Golon, Agnieszka Karczyńska, Paweł Krupa, Magdalena A. Mozolewskae, Mariusz Makowski, Robert Ganzynkowicz, Artur Giełdoń, Maciej Maciejczyk
    Book:
    Progress in Molecular Biology and Translational Science. Computational Approaches for Understanding Dynamical Systems: Protein Folding and Assembly (rok: 2020, tom: 170, strony: 73-122), Wydawca: Elsevier
    Status:
    Published

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