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Increasing global and local accuracy of the coarse-grained UNRES model of proteins and its extensions to simulating very large protein systems and racemization of amino-acid residues.

2017/25/B/ST4/01026

Keywords

Descriptors

  • ST4_15: Chemia teoretyczna i obliczeniowa
  • ST4_4: Struktura i architektura molekularna
  • ST3_17: Fizyka statystyczna (materii skondensowanej)

Panel

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

Host institution

Uniwersytet Gdański, Wydział Chemii

Voivodeship: 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: 7

Call

OPUS 13 – announced on 2017-03-15

Amount awarded
739 200 PLN
Project start date
2018-01-03
Project end date
2021-06-02
Project duration
41 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. Zestaw do archiwizacji danych: streamer obsługujący techologię LTO-7, pojemność taśmy 6TB oraz 20 taśm. Cost: 21 000 PLN

Information in the final report

Publication in academic press/journals (16)

  1. 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, Cezary Czaplewski
    Academic press:
    Journal of Chemical Information and Modeling (year: 2020, volume: 60, pages: 1844−1864), Publisher: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.9b00864 – link to the publication

  2. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scaleconsistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation

    Authors:
    Adam Liwo, Adam K. Sieradzan, Agnieszka G. Lipska, Cezary Czaplewski, InSuk Joung, Wioletta Żmudzińska, Anna Hałabis, Stanisław Ołdziej
    Academic press:
    Journal of Chemical Physics (year: 2019, volume: 150, pages: 155104-1 - 155104-24), Publisher: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.5093015 – link to the publication

  3. 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, Magdalena Ślusarz, Silvia N. Crivelli, Adam Liwo
    Academic press:
    Journal of Molecular Graphics and Modeling (year: 2019, volume: 92, pages: 154-166), Publisher: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2019.07.013 – link to the publication

  4. Pseudopotentials for coarse-grained cross-link-assisted modeling of protein structures

    Authors:
    Mateusz Kogut, Zhou Gong, Chun Tang, Adam Liwo
    Academic press:
    Journal of Computational Chemistry (year: 2021, volume: 0, pages: 13881), Publisher: John Wiley & Sons
    Status:
    Published
    DOI:
    10.1002/jcc.26736 – link to the publication

  5. Large-scale simulations in chemistry and biochemistry

    Authors:
    Adam Liwo
    Academic press:
    TASK Quarterly (year: 2018, volume: 22, pages: 46033), Publisher: TASK Publishing
    Status:
    Published
    DOI:
    10.17466/tq2018/22.4/g – link to the publication

  6. Introduction of a Bounded Penalty Function in Contact-Assisted Simulations of Protein Structures to Omit False Restraints

    Authors:
    Emilia A. Lubecka, Adam Liwo
    Academic press:
    Journal of Computational Chemistry (year: 2019, volume: 40, pages: 2164–2178), Publisher: Wiley
    Status:
    Published
    DOI:
    10.1002/jcc.25847 – link to the publication

  7. 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 (year: 2019, volume: 87, pages: 1283–1297), Publisher: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.25816 – link to the publication

  8. 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 (year: 2020, volume: 152, pages: 54902), Publisher: American Physical Society
    Status:
    Published
    DOI:
    10.1063/1.5138991 – link to the publication

  9. High Performance Computing with Coarse Grained Model of Biological Macromolecules

    Authors:
    Emilia Lubecka, Adam Sieradzan, Cezary Czaplewski, Pawe l Krupa, Adam Liwo
    Academic press:
    Supercomputing Frontiers and Innovations (year: 2018, volume: 5, pages: 63-75), Publisher: Publishing Center of South Ural State University
    Status:
    Published
    DOI:
    10.14529/jsfi180206 – link to the publication

  10. 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 (year: 2018, volume: 46, pages: W304–W309), Publisher: Oxford Univ. Press
    Status:
    Published
    DOI:
    10.1093/nar/gky328 – link to the publication

  11. Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment

    Authors:
    A. Antoniak, I. Biskupek, K.K. Bojarski, C. Czaplewski, A. Giełdoń, M. Kogut, M.M. Kogut, P. Krupa, A.G. Lipska, A. Liwo, E.A. Lubecka, M. Marcisz, M. Maszota-Zieleniak, S.A. Samsonov, A.K. Sieradzan, M.J. Ślusarz, R. Ślusarz, P.A. Wesołowski, K. Zięba
    Academic press:
    Journal of Molecular Graphics and Modeling (year: 2021, volume: 108, pages: 108008), Publisher: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2021.108008 – link to the publication

  12. Unfolding the prospects of computational (bio)materials modeling

    Authors:
    G. J. Agur Sevink, Jozef Adam Liwo, Pietro Asinari, Donal MacKernan, Giuseppe Milano, Ignacio Pagonabarraga
    Academic press:
    Journal of Chemical Physics (year: 2020, volume: 153, pages: 100901), Publisher: American Physical Society
    Status:
    Published
    DOI:
    10.1063/5.0019773 – link to the publication

  13. Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models

    Authors:
    Karolina Zięba, Cezary Czaplewski, Adam Liwo, Giuseppe Graziano
    Academic press:
    Physical Chemistry Chemical Physics (year: 2020, volume: 22, pages: 4758-4771), Publisher: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c9cp06627f – link to the publication

  14. ESCASA: Analytical estimation of atomic coordinates from coarse-grained geometry for nuclear-magnetic-resonance-assisted protein structure modeling. I. Backbone and Hβ protons

    Authors:
    Emilia Lubecka, Adam Liwo
    Academic press:
    Journal of Computational Chemistry (year: 2021, volume: 42, pages: 1579-1589), Publisher: John Wiley & Sons
    Status:
    Published
    DOI:
    10.1002/jcc.26695 – link to the publication

  15. Modeling SARS-CoV2 proteins in the CASP-commons experiment

    Authors:
    Andriy Kryshtafovych, John Moult, Dennis Della Corte, Krzysztof Fidelis, Sohee Kwon, Kliment Olechnovič, Chaok Seok, Česlovas Venclovas, Jonghun Won, collaborative authors
    Status:
    Accepted for publication

  16. Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment

    Authors:
    Marc F Lensink, Guillaume Brysbaer, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphael AG 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 G Lipska, Adam Liwo, Emilia A Lubecka, Martyna Maszota-Zieleniak, Adam K Sieradzan, Rafał Ślusarz, Patryk A Wesołowski, Karolina Zięba, Carlos A Del Carpio Muñoz, Eiichiro Ichiishi, Ameya Harmalkar, Jeffrey J Gray, Alexandre MJJ 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 Sun1, Usman Ghani, Nasser Hashemi, Sandor Vajda, Dima Kozakov, Mireia Rosell, Luis A Rodríguez-Lumbreras, Juan Fernandez-Recio, Agnieszka Karczynska, 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, Shuang Zhang, Xiaoqin Zou, Shoshana J Wodak
    Status:
    Accepted for publication

Book publications / chapters in book publications (4)

  1. 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, Cezary Czaplewski
    Book:
    Methods in Molecular Biology: Protein Supersecondary Structures: Methods and Protocols (year: 2019, volume: 1958, pages: 133-145), Publisher: Springer Science+Business Media, LLC,
    Status:
    Published

  2. 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 (year: 2020, volume: 170, pages: 74-122), Publisher: Academic Press, Elsevier
    Status:
    Published

  3. Physics-based coarse-grained modeling in bio- and nanochemistry

    Authors:
    Adam Liwo, Adam K. Sieradzan, Agnieszka S. Karczyńska, Emilia A. Lubecka, Sergey A. Samsonov, Cezary Czaplewski, Paweł Krupa, Magdalena Mozolewska
    Book:
    Practical Aspects of Computational Chemistry (year: 2021, volume: V, pages: 46049), Publisher: Springer
    Status:
    Accepted for publication

  4. Probing Protein Aggregation Using the Coarse-Grained UNRES Force Field

    Authors:
    Ana V. Rojas, Gia G. Maisuradze, Harold A. Scheraga, Adam Liwo
    Book:
    Computer Simulations of Aggregation of Proteins and Peptides: Methods and Protocols (year: 2021, volume: 0, pages: 15707), Publisher: Springer
    Status:
    Accepted for publication

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Graphic design and implementation: Jakub Piotrowski