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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Enhancing resolution and predictive power of the UNRES force field for protein folding simulations by revision of the potentials of interactions involving protein main chain

2011/01/N/ST4/01772

Keywords:

UNRES force field hydrogen bond cis-trans isomerization shielding effect

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: 2

Call: PRELUDIUM 1 - announced on 2011-03-15

Amount awarded: 150 000 PLN

Project start date (Y-m-d): 2011-12-13

Project end date (Y-m-d): 2014-12-12

Project duration:: 36 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Switch (9 537 PLN)
  2. Zestawy komputerowe do klastra obliczeniowego wraz z monitorami do obsługi klastra (8 szt.) (32 000 PLN)
  3. Komputery (18 040 PLN)
  4. UPS (50 400 PLN)
  5. tablet.

Information in the final report

  • Publication in academic press/journals (6)
  1. Improvement of the Treatment of Loop Structures in the UNRES Force Field by Inclusion of Coupling between Backbone- and Side-Chain-Local Conformational States
    Authors:
    Paweł Krupa, Adam K. Sieradzan, S. Rackovsky, Maciej Baranowski, Stanisław Ołdziej, Harold A. Scheraga, Adam Liwo, and Cezary Czaplewski
    Academic press:
    J. Chem. Theory Comput. (rok: 2013, tom: 9, strony: 4620–4632), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/ct4004977 - link to the publication
  2. 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, and Harold A. Scheraga
    Academic press:
    Proceedings of the National Academy of Sciences of the United States of America PNAS (rok: 2013, tom: 110, strony: 14936–14941), Wydawca: National Academy of Sciences
    Status:
    Published
    DOI:
    10.1073/pnas.1313316110 - link to the publication
  3. Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the united residue (UNRES) force field for protein simulations
    Authors:
    Adam K. Sieradzan , Pawel Krupa , Harold A.Scheraga , Adam Liwo , and Cezary Czaplewski
    Academic press:
    J. Chem. Theory Comput. (rok: 2015, tom: Just Accepted, strony: nie dotyczy), Wydawca: ACS Publications
    Status:
    Accepted for publication
    DOI:
    10.1021/ct500736a - link to the publication
  4. WeFold:Acoopetitionforprotein structureprediction
    Authors:
    George A. Khoury, Adam Liwo, Firas Khatib, Hongyi Zhou, Gaurav Chopra, Jaume Bacardit, 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 , and 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
  5. Extension of UNRES Force Field to Treat Polypeptide Chains with d-Amino Acid Residues
    Authors:
    Adam K. Sieradzan, Ulrich H. E. Hansmann, Harold A. Scheraga, and Adam Liwo
    Academic press:
    J. Chem. Theory Comput. (rok: 2012, tom: 8(11), strony: 4746-4757), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/ct3005563 - link to the publication
  6. Folding and Self-Assembly of a Small Protein Complex
    Authors:
    Adam K. Sieradzan, Adam Liwo, and Ulrich H. E. Hansmann
    Academic press:
    J. Chem. Theory Comput. (rok: 2012, tom: 8(9), strony: 3416-3422), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/ct300528r - link to the publication

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