Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions

2012/06/A/ST4/00376

Keywords:

proteins nucleic acids polysaccharides coarse-grained models potentials of mean force multipole-multipole interactions molecular dynamics thermodynamical properties

Descriptors:

  • ST4_15: Colloid chemistry
  • ST4_4: Theoretical and computational chemistry
  • ST3_17: Other related subjects

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 Liwo 

Number of co-investigators in the project: 9

Call: MAESTRO 3 - announced on 2012-06-15

Amount awarded: 1 071 480 PLN

Project start date (Y-m-d): 2013-03-26

Project end date (Y-m-d): 2018-03-25

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

Project status: Project settled

Equipment purchased [PL]

  1. Kable, gniazdka, wtyczki elektryczne, kable eternetowe, inny drobny sprzęt elektryczny (800 PLN)
  2. Macbook.
  3. Switch 24-portowy (3 700 PLN)
  4. Laptop Dell.
  5. Przenośny klimatyzator (37 kW) (3 000 PLN)
  6. Rack na max. 20 nodów (2 500 PLN)
  7. brak danych.
  8. Laptop ASUS.
  9. Nod obliczeniowy; 1 U Intel dual CPU SC815R; 2x Intel Xeon 6-Core E5645 2.40 GHz 12MB 5.86 GT/s (Westmere); 24 GB ECC Registered DDR3 RAM 2Rank ATP (6x 4096 MB); osłona przednia (16 szt.) (152 000 PLN)

Information in the final report

  • Publication in academic press/journals (18)
  • Book publications / chapters in book publications (2)
  1. Kinks, loops, and protein folding, with protein A as an example
    Authors:
    Andrey Krokhotin, Adam Liwo, Gia G. Maisuradze, Antti J. Niemi, Harold A. Scheraga
    Academic press:
    Journal of Chemical Physics (rok: 2014, tom: 140, strony: 25101), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4855735 - link to the publication
  2. WeFold: A coopetition for protein structure prediction
    Authors:
    George A. Khoury, Adam Liwo, Firas Khatib, Hongyi Zhou, Gaurav Chopra, Jaume Bacardit,7 Leandro O. Bortot, Rodrigo A. Faccioli, Xin Deng, Yi He, Pawel Krupa, Jilong Li, Magdalena A. Mozolewska, Adam K. Sieradzan, James Smadbeck, Tomasz Wirecki, Seth Cooper, Jeff Flatten, Kefan Xu, David Baker, Jianlin Cheng, Alexandre C. B. Delbem, Christodoulos A. Floudas, Chen Keasar, Michael Levitt, Zoran Popovic, Harold A. Scheraga, Jeffrey Skolnick, Silvia N. Crivelli , Foldit Players
    Academic press:
    Proteins: Structure, Function, and Bioinformatics (rok: 2014, tom: 82, strony: 1850–1868), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.24538 - link to the publication
  3. A maximum-likelihood approach to force-field calibration
    Authors:
    Bartłomiej Zaborowski, Dawid Jagieła, Cezary Czaplewski, Anna Hałabis, Agnieszka Lewandowska, Wioletta Żmudzińska, Stanisław Ołdziej, Agnieszka Karczyńska, Christian Omieczynski, Tomasz Wirecki, Adam Liwo
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2017, tom: 55, strony: 2050-2070), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.5b00395 - link to the publication
  4. A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields
    Authors:
    A.K. Sieradzan, A. Giełdoń, Y. Yin, Y. He, H.A. Scheraga, A. Liwo
    Academic press:
    Journal of Computational Chemistry (rok: 2018, tom: 39, strony: 2360-2370), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/jcc.25571 - link to the publication
  5. Common functionally important motions of the nucleotide-binding domain of Hsp70
    Authors:
    Ewa I. Gołaś, Cezary Czaplewski, Harold A. Scheraga, Adam Liwo
    Academic press:
    Proteins: Structure, Function and Bioinformatics (rok: 2015, tom: 83, strony: 282-299), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.24731 - link to the publication
  6. Mean-Field Interactions between Nucleic-Acid-Base Dipoles can Drive the Formation of a Double Helix
    Authors:
    Yi He, Maciej Maciejczyk, Stanisław Ołdziej, Harold A. Scheraga, Adam Liwo
    Academic press:
    Physical Review Letters (rok: 2013, tom: 110, strony: 98101), Wydawca: American Physical Society
    Status:
    Published
    DOI:
    10.098101 - link to the publication
  7. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction
    Authors:
    Agnieszka G. Lipska, Steven R. Seidman, Adam K. Sieradzan, Artur Giełdoń, Adam Liwo, Harold A. Scheraga
    Academic press:
    Journal of Chemical Physics (rok: 2016, tom: 144, strony: 184110), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4948710 - link to the publication
  8. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains
    Authors:
    A.K. Sieradzan, M. Makowski, A. Augustynowicz, A. Liwo
    Academic press:
    Journal of Chemical Physics (rok: 2017, tom: 146, strony: 124106), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4978680 - link to the publication
  9. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. II. Backbone-local potentials of coarse-grained O1->4-bonded polyglucose chains
    Authors:
    E.A. Lubecka, A. Liwo
    Academic press:
    Journal of Chemical Physics (rok: 2017, tom: 147, strony: 115101), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4994130 - link to the publication
  10. Coarse graining: a tool for large-scale simulations or more?
    Authors:
    Adam Liwo
    Academic press:
    Physica Scripta (rok: 2013, tom: 87, strony: 58502), Wydawca: IOP Publishing LTD
    Status:
    Published
    DOI:
    10.1088/0031-8949/87/05/058502 - link to the publication
  11. Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
    Authors:
    Paweł Krupa, Magdalena A. Mozolewska, Marta Wiśniewska, Yanping Yin, Yi He, Adam K. Sieradzan, Robert Ganzynkowicz, Agnieszka G. Lipska, Agnieszka Karczyńska, Magdalena Ślusarz, Rafał Ślusarz, Artur Giełdoń, Cezary Czaplewski, Dawid Jagieła, Bartłomiej Zaborowski, Harold A. Scheraga, and Adam Liwo
    Academic press:
    Bioinformatics (rok: 2016, tom: 32, strony: 3270–3278), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btw404 - link to the publication
  12. A unified coarse-grained model of biological macromolecules based on mean-field multipole–multipole interactions
    Authors:
    Adam Liwo, Maciej Baranowski, Cezary Czaplewski, Ewa Gołaś, Yi He, Dawid Jagieła, Paweł Krupa, Maciej Maciejczyk, Mariusz Makowski, Magdalena A. Mozolewska, Andrei Niadzvedtski, Stanisław Ołdziej, Harold A. Scheraga, Adam K. Sieradzan, Rafał Ślusarz, Tomasz Wirecki, Yanping Yin, Bartłomiej Zaborowski
    Academic press:
    Journal of Molecular Modeling (rok: 2014, tom: 20, strony: 2306-1 - 2306-5), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s00894-014-2306-5 - link to the publication
  13. Dynamics of disulfide-bond disruption and formation in the thermal unfolding of ribonuclease A
    Authors:
    P. Krupa, A.K. Sieradzan, M.A. Mozolewska, H. Li, A. Liwo, H.A. Scheraga
    Academic press:
    Journal of Chemical Theory and Computation (rok: 2017, tom: 13, strony: 5721-5730), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jctc.7b00724 - link to the publication
  14. Optimization of a Nucleic Acids united-RESidue 2- Point model (NARES-2P) with a maximum-likelihood approach.
    Authors:
    Yi He, Adam Liwo, Harold A. Scheraga
    Academic press:
    Journal of Chemical Physics (rok: 2015, tom: 143, strony: 243111), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4932082 - link to the publication
  15. Physics-based Potentials for coarse-grained modeling of protein DNA interactions
    Authors:
    Yanping Yin, Adam K. Sieradzan, Adam Liwo, Yi He, Harold A. Scheraga
    Academic press:
    Journal of Chemical Theory and Computation (rok: 2015, tom: 11, strony: 1792-1808), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/ct5009558 - link to the publication
  16. Lessons from application of the UNRES force field to predictions of structures of CASP10 targets
    Authors:
    Yi He, Magdalena A. Mozolewska, Paweł Krupa, Adam K. Sieradzan, Tomasz K. Wirecki, Adam Liwo, Khatuna Kachlishvili, Shalom Rackovsky, Dawid Jagieła, Rafał Ślusarz, Cezary R. Czaplewski, Stanisław Ołdziej, Harold A. Scheraga
    Academic press:
    Proceedings of the National Academy of Sciences of the United States of America (rok: 2013, tom: 110, strony: 14937-14941), Wydawca: National Academy of Sciences
    Status:
    Published
    DOI:
    10.1073/pnas.1313316110 - link to the publication
  17. Prediction of DNA and RNA Structure with the NARES- 2P Force Field and Conformational Space Annealing
    Authors:
    A.K. Sieradzan, Ł. Golon, A. Liwo
    Academic press:
    Physical Chemisty and Chemical Physics (rok: 2018, tom: 20, strony: 19656-19663), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c8cp03018a - link to the publication
  18. Studies of conformational changes of an arginine-binding protein from Thermotoga maritima in the presence and absence of ligand via molecular dynamics simulations with the coarse-grained UNRES force field
    Authors:
    Agnieszka G. Lipska, Adam K. Sieradzan, Paweł Krupa, Magdalena A. Mozolewska, Sabato D'Auria, Adam Liwo
    Academic press:
    Journal of Molecular Modeling (rok: 2015, tom: 21, strony: /s00894-015-2609-1 - /s00894-015-2609-5), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s00894-015-2609-1 - link to the publication
  1. Microscopic Physics-Based Models of Proteins and Nucleic Acids UNRES and NARES
    Authors:
    Maciej Baranowski, Cezary Czaplewski, Ewa I. Gołaś, Yuan-Jie He, Dawid Jagieła, Paweł Krupa, Adam Liwo, Gia G. Maisuradze, Mariusz Makowski, Magdalena A. Mozolewska, Andrei Niadzvedtski, Antti J. Niemi, Shelly Rackovsky, RafałŚlusarz, Adam K. Sieradzan, Stanisław Ołdziej, Tomasz Wirecki, Yanping Yin, Bartłomiej Zaborowski, Harold A. Scheraga
    Book:
    Coarse-Grained Models of Biomolecules (rok: 2018, tom: 1, strony: 65-116), Wydawca: CRC Press,
    Status:
    Published
  2. A Novel Coarse-Grained Description of Protein Structure and Folding by UNRES Force Field and Discrete Nonlinear Schrödinger Equation
    Authors:
    Adam Liwo, Antti Niemi, Xubiao Peng, Adam K. Sieradzan
    Book:
    Frontiers in Computational Chemistry (rok: 2015, tom: 1, strony: 257-289), Wydawca: Bentham Science Publications
    Status:
    Published

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