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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DNA repair mechanisms: from coarse-grained to atomistic description

2015/17/D/ST4/00509

Keywords:

DNA coarse-grained force field all-atom force field

Descriptors:

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

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: 2

Call: SONATA 9 - announced on 2015-03-16

Amount awarded: 314 200 PLN

Project start date (Y-m-d): 2016-01-25

Project end date (Y-m-d): 2018-01-24

Project duration:: 24 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. Komputer biurowy (5 000 PLN)
  2. Nod obliczeniowy do klastra (2 szt.) (50 000 PLN)
  3. Tablet.
  4. Akcesoria komputerowe do budowy komputera do klastra (5 623 PLN)

Information in the final report

  • Publication in academic press/journals (6)
  • Book publications / chapters in book publications (2)
  1. Shielding effect in protein folding
    Authors:
    Adam K. Sieradzan, Agnieszka G. Lipska, Emilia A. Lubecka
    Academic press:
    Journal of Molecular Graphics and Modelling (rok: 2018, tom: 79, strony: 118-132), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.018 - link to the publication
  2. Computational Studies of the Mechanical Stability of Single-Strand Break DNA
    Authors:
    Pawel Krupa, David Wales, Adam Sieradzan
    Academic press:
    J. Phys Chem. B (rok: 2018, tom: 122, strony: 8166-8173), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.8b05417 - link to the publication
  3. A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields
    Authors:
    Adam K. Sieradzan, Artur Gie ldoń, Yanping Yin, Yi He, Harold A. Scheraga, Adam Liwo
    Academic press:
    J. Comput Chem. (rok: 2018, tom: 39, strony: 2360-2370), Wydawca: Wiley Online Library
    Status:
    Published
    DOI:
    10.1002/jcc.2557 - link to the publication
  4. Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing
    Authors:
    Adam K. Sieradzan, Łukasz Golon, Adam Liwo
    Academic press:
    Physical Chemistry Chemical Physics (rok: 2018, tom: 20, strony: 19656-19663), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c8cp03018a - link to the publication
  5. Introduction of Steered Molecular Dynamics into UNRES Coarse-Grained Simulations Package
    Authors:
    Adam K. Sieradzan* and Rafał Jakubowski
    Academic press:
    J. Comput. Chem. (rok: 2017, tom: 38, strony: 553-562), Wydawca: Wiley Online Library
    Status:
    Published
    DOI:
    10.1002/jcc.24685 - link to the publication
  6. What Makes Telomeres Unique?
    Authors:
    Adam Kazimierz Sieradzan, Pawel Krupa, and David J. Wales
    Academic press:
    J. Phys. Chem. B, (rok: 2017, tom: 121, strony: 2207-2219), Wydawca: ACS Publication
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.6b08780 - 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 Karczyńska, Agnieszka Lipska, Emilia A. Lubecka, Ewa Gołaś, Tomasz Wirecki, Mariusz Makowski, Stanisław Ołdziej, Adam Liwo
    Book:
    Methods in molecular biology (rok: 2018, ), Wydawca: Springer
    Status:
    Submitted
  2. Formation of Secondary and Supersecondary Structure of Proteins as a Result of Coupling Between Local and Backbone-Electrostatic Interactions: A View Trough Cluster-Cumulant Scope
    Authors:
    Adam Liwo, Adam K. Sieradzan, Cezary Czaplewski
    Book:
    Protein Supersecondary Structures (rok: 2019, ), Wydawca: Springer
    Status:
    Published

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