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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Enabling routine and reliable analysis of transport tunnels in proteins

2017/25/B/NZ1/01307

Keywords:

tunnels dynamics molecular transport protein function

Descriptors:

  • NZ1_3: Biophysics
  • NZ1_4: Structural biology
  • NZ2_7: Bioinformatics

Panel:

NZ1 - Molecular biology, structural biology, biotechnology: molecular biology, structural biology, biotechnology

Host institution :

Międzynarodowy Instytut Biologii Molekularnej i Komórkowej

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Jan Brezovsky 

Number of co-investigators in the project: 4

Call: OPUS 13 - announced on 2017-03-15

Amount awarded: 1 375 050 PLN

Project start date (Y-m-d): 2018-10-01

Project end date (Y-m-d): 2022-11-30

Project duration:: 50 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. GPU obliczeniowej stacji roboczych / węzłów. (3 szt.) (99 000 PLN)
  2. Komputer przeznaczony do modelowania molekularnego.
  3. Oprogramowanie AMBER.
  4. Komputer przeznaczony do modelowania molekularnego (10 000 PLN)
  5. Macierz dyskowa (16 352 PLN)
  6. Serwer internetowy (20 000 PLN)

Information in the final report

  • Publication in academic press/journals (5)
  • Articles in post-conference publications (1)
  1. Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations
    Authors:
    Sequeiros-Borja C, Surpeta B, Marchlewski I, Brezovsky J
    Academic press:
    MethodsX (rok: 2023, tom: 10C, strony: 101968), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.mex.2022.101968 - link to the publication
  2. Common Dynamic Determinants Govern Quorum Quenching Activity in N-Terminal Serine Hydrolases
    Authors:
    Surpeta B, Grulich M, Palyzová A, Marešová H, Brezovsky J
    Academic press:
    ACS Catalysis (rok: 2022, tom: 12, strony: 6359-6374), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acscatal.2c00569 - link to the publication
  3. Dynamics, a Powerful Component of Current and Future inSilico Approaches for Protein Design and Engineering
    Authors:
    Surpeta B, Sequeiros-Borja CE, Brezovsky J
    Academic press:
    International Journal ofMolecular Sciences (rok: 2020, tom: 21(8), strony: 2713), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms21082713 - link to the publication
  4. Recent advances in user-friendly computational tools to engineer protein function
    Authors:
    Sequeiros-Borja CE, Surpeta B, Brezovsky J
    Academic press:
    Briefings in Bioinformatics (rok: 2020, tom: brak, strony: brak), Wydawca: OXFORD UNIV PRESS
    Status:
    Published
    DOI:
    10.1093/bib/bbaa150 - link to the publication
  5. TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them
    Authors:
    Brezovsky J, Thirunavukarasu AS, Surpeta B, Sequeiros-Borja CE, Mandal N, Sarkar DK, Dongmo Foumthuim CJ, Agrawal N
    Academic press:
    Bioinformatics (rok: 2022, tom: 38, strony: 1752-1753), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinfo - link to the publication
  1. Exploring rare events of water transport in and out of buried active sites of hydrolytic enzymes
    Authors:
    Thirunavukarasu AS, Dongmo Foumthuim CJ, Brezovsky J
    Conference:
    45th FEBS Congress, Molecules of Life: Towards New Horizons (rok: 2021, ), Wydawca: FEBS Press
    Data:
    konferencja 3-8 Lipiec
    Status:
    Published

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