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Design, parametrization and implementation of potentials of amino acid side chain interactions in water for application in large-scale protein simulations

2013/10/E/ST4/00755

Keywords

Descriptors

  • ST4_4: Struktura i architektura molekularna
  • ST4_15: Chemia teoretyczna i obliczeniowa

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)

dr hab. Mariusz Makowski

Number of co-investigators in the project: 3

Call

SONATA BIS 3 – announced on 2013-06-14

Amount awarded
595 200 PLN
Project start date
2014-05-05
Project end date
2018-05-04
Project duration
48 months (the same as in the proposal)
Project status
Project settled

Equipment purchased [PL]

  1. 20 nodów z 12-rdzeniowym procesorem Intel Xenon. Cost: 200 000 PLN

Information in the final report

Publication in academic press/journals (6)

  1. A Unified Coarse-Grained Model of Biological Macromolecules Based on Mean-Field Multipole-Multipole Interactions

    Authors:
    A. Liwo, M. Baranowski, C. Czaplewski, E. Gołaś, Y. He, D. Jagieła, P. Krupa, M. Maciejczyk, M. Makowski, M. Mozolewska, A. Niadzvedtski, Stanisław Ołdziej, H. A. Scheraga, A.K. Sieradzan, R. Ślusarz, T. Wirecki, Y. Yin, B. Zaborowski
    Academic press:
    Journal of Molecular Modelling (year: 2014, volume: 20, pages: 2306), Publisher: Springer
    Status:
    Published
    DOI:
    10.1007/s00894-014-2306-5 – link to the publication

  2. Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VII. Charged – hydrophobic/polar and polar – hydrophobic/polar side chains.

    Authors:
    M. Makowski, A. Liwo, H.A, Scheraga
    Academic press:
    Journal of Physical Chemistry B (year: 2017, volume: 121, pages: 379-390), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.6b08541 – link to the publication

  3. 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 (year: 2017, volume: 146, pages: 124106), Publisher: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4978680 – link to the publication

  4. Theoretical studies of interactions between O-phosphorylated and standard amino-acid side-chain models in water

    Authors:
    M. Wiśniewska, E. Sobolewski, S. Ołdziej, A. Liwo, H.A. Scheraga, M. Makowski
    Academic press:
    Journal of Physical Chemistry B (year: 2015, volume: 119, pages: 8526-8534), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.5b04782 – link to the publication

  5. Theoretical studies on the anionic association of phenol and its derivatives in acetonitrile

    Authors:
    M. Wiśniewska, M. Makowski
    Academic press:
    Journal of Molecular Strcuture (year: 2014, volume: 1076, pages: 165-173), Publisher: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.molstruc.2014.07.056 – link to the publication

  6. Introduction of Phosphorylated Residues into the UNRES Coarse- Grained Model: Toward Modeling of Signaling Processes

    Authors:
    A. K. Sieradzan, M. Bogunia, P. Mech, R. Ganzynkowicz, A. Giełdoń, A. Liwo, M. Makowski
    Academic press:
    Journal of Physical Chemistry B (year: 2019, volume: 123, pages: 5721-5729), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jpcb.9b03799 – link to the publication

Articles in post-conference publications (10)

  1. Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. Polar-polar/hydrophobic side-chains

    Authors:
    A. Głębocka, P. Mech, M. Bogunia, M. Ogryzek, A. Chylewska, A. Liwo, M. Makowski
    Conference:
    Central European School on Physical Organic Chemistry Movement in Chemistry (year: 2016, pages: 56), Publisher: UWr
    Date:
    conference 6-10 June
    Status:
    Published

  2. Simple analytical formulas for the potentials of mean force of interactions between O-phosphorylated and hydrphobic amino-acid side-chain models in water

    Authors:
    R. Ganzynkowicz, A. Głębocka, A. Liwo, M. Makowski
    Conference:
    Second Polish-Korean Conference on Protein Folding, Theoretical and Experimental Approaches (year: 2016, pages: 62), Publisher: UG
    Date:
    conference 28.05-01.06
    Status:
    Published

  3. Physics-based interaction potentials of O-phosphorylated serine and hydrophobic side-chains of amino acids for coarse-grained force-fields

    Authors:
    M. Wiśniewska, A. Bartosik, M. Ogryzek, M. Makowski
    Conference:
    The First Korean-Polish Conference on Protein Folding: Theoretical and Experimental Approaches, KIAS, Seoul, Korea (year: 2015, pages: 43), Publisher: KIAS
    Date:
    conference 24-28 May
    Status:
    Published

  4. Poszukiwania analitycznych wyrażeń opisujących oddziaływania O-fosforylowanych łańcuchów bocznych reszt aminokwasowych z aminokwasami

    Authors:
    M. Makowski, A. Liwo, H. A. Scheraga
    Conference:
    58 Zjazd Naukowy Polskiego Towarzystwa Chemicznego w Gdańsku, Gdańsk (year: 2015, pages: S09KS01), Publisher: PTCH
    Date:
    conference 21-25 wrzesień
    Status:
    Published

  5. Potencjał oddziaływań pomiędzy O-fosforylowaną tyrozyną a modelami polarnych łańcuchów bocznych reszt aminokwasowych w wodzie.

    Authors:
    R. Ganzynkowicz, A. Głębocka, A. Liwo, M. Makowski
    Conference:
    59 Zjazd Naukowy Polskiego Towarzystwa Chemicznego w Poznaniu (year: 2016, pages: 235), Publisher: Polskie Towarzystwo Chemiczne
    Date:
    conference 19-23 wrzesień
    Status:
    Published

  6. ODDZIAŁYWANIA POMIĘDZY O-FOSFORYLOWANYMI AMINOKWASAMI A MODELAMI ŁAŃCUCHÓW BOCZNYCH RESZT AMINOKWASOWYCH W WODZIE - STUDIA TEORETYCZNE

    Authors:
    Robert Ganzynkowicz, Adam Liwo, Mariusz Makowski
    Conference:
    60. Zjazd Naukowy Polskiego Towarzystwa Chemicznego (year: 2017, pages: S07K10), Publisher: PTCH
    Date:
    conference 17-21 września
    Status:
    Published

  7. Potencjał opisujący oddziaływania pomiędzy O-fosforylowanymi aminokwasami z modelami hydrofobowych łańcuchów bocznych reszt aminokwasowych w wodzie.

    Authors:
    M. Makowski, A. Głębocka, R. Ganzynkowicz, A. Liwo
    Conference:
    59 Zjazd Naukowy Polskiego Towarzystwa Chemicznego w Poznaniu (year: 2016, pages: 234), Publisher: Polskie Towarzystwo Chemiczne
    Date:
    conference 19-23 wrzesień
    Status:
    Published

  8. On the Development of Side Chain - Side Chain Interaction Potentials in Amino Acids to Be Used for Protein-Folding.

    Authors:
    Mariusz Makowski
    Conference:
    BIT's 6th Annual Conference of AnalytiX-2018 (year: 2018, pages: 101), Publisher: Analytix
    Date:
    conference 26-28.03
    Status:
    Published

  9. Side chain – side chain interaction potentials

    Authors:
    M. Makowski, A. Liwo, H. A. Scheraga
    Conference:
    The First Korean-Polish Conference on Protein Folding: Theoretical and Experimental Approaches, KIAS, Seoul, Korea (year: 2015, pages: 27), Publisher: KIAS
    Date:
    conference 24-28 May
    Status:
    Published

  10. Analytical Formulas for the Potentials of Mean Force of the Interaction of O-phosphorylated and Hydrophobic Amino-Acid Side Chains in Water

    Authors:
    M. Wiśniewska, A. Liwo, M. Makowski
    Conference:
    19th Annual International Conference on Research in Computational Molecular Biology – RECOMB 2015 (year: 2015, pages: 39-40), Publisher: RECOMB
    Date:
    conference April 12-15
    Status:
    Published

Book publications / chapters in book publications (1)

  1. Physics-based modeling of side chain –side chain interactions in the UNRES force field.

    Authors:
    Mariusz Makowski
    Book:
    Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes (year: 2019, pages: 89-115), Publisher: Springer Nature
    Status:
    Accepted for publication

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