Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

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Combining Rosetta method with deeply coarse grained SURPASS model into a novel multiscale algorithm for modeling proteins and their complexes

2018/29/B/ST6/01989

Keywords:

molecular modeling protein modeling flexible protein docking

Descriptors:

  • ST6_12: Scientific computing, simulation and modelling tools
  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

Host institution :

Uniwersytet Warszawski, Wydział Chemii

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Dominik Gront 

Number of co-investigators in the project: 4

Call: OPUS 15 - announced on 2018-03-15

Amount awarded: 828 400 PLN

Project start date (Y-m-d): 2019-01-31

Project end date (Y-m-d): 2022-12-30

Project duration:: 47 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. Dodatkowa stacja robocza - laptop.
  2. stacje robocze lub laptopy (3 szt.) (24 000 PLN)
  3. Serwer obliczeniowy (2 szt.) (44 729 PLN)

Information in the final report

  • Publication in academic press/journals (17)
  1. An Unprecedented Number of Cytochrome P450s Are Involved in Secondary Metabolism in Salinispora Species
    Authors:
    Nsikelelo Allison Malinga, Nomfundo Nzuza, Tiara Padayachee, Puleng Rosinah Syed, Rajshekhar Karpoormath, Dominik Gront, David R. Nelson, Khajamohiddin Syed
    Academic press:
    Microorganisms (rok: 2022, tom: 10, strony: 871), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/microorganisms10050871 - link to the publication
  2. Analysis of protein structures containing HEPES and MES molecules
    Authors:
    Joanna Magdalena Macnar, Dariusz Brzezinski, Maksymilian Chruszcz, Dominik Gront
    Academic press:
    Protein Science (rok: 2022, tom: 31, strony: e4415), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/pro.4415 - link to the publication
  3. Automated Protein Secondary Structure Assignment from Cα Positions Using Neural Networks
    Authors:
    Mohammad N. Saqib, Justyna D. Kryś, Dominik Gront
    Academic press:
    Biomolecules (rok: 2022, tom: 12, strony: 841), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom12060841 - link to the publication
  4. BioShell 3.0: Library for processing structural biology data.
    Authors:
    Joanna M. Macnar, Natalia A. Szulc , Justyna D. Krys ́, Aleksandra E. Badaczewska-Dawid and Dominik Gront
    Academic press:
    Biomolecules (rok: 2020, tom: 10, strony: 461), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/biom10030461 - link to the publication
  5. Contrasting Health Effects of Bacteroidetes and Firmicutes Lies in Their Genomes: Analysis of P450s, Ferredoxins, and Secondary Metabolite Clusters
    Authors:
    Bridget Valeria Zinhle Nkosi, Tiara Padayachee, Dominik Gront, David R. Nelson, Khajamohiddin Syed
    Academic press:
    Int. J. Mol. Sci. (rok: 2022, tom: 23, strony: 5057), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms23095057 - link to the publication
  6. Diversification of Ferredoxins across Living Organisms
    Authors:
    Nomfundo Nzuza, Tiara Padayachee , Wanping Chen , Dominik Gront , David R. Nelson and Khajamohiddin Syed
    Academic press:
    Curr. Issues Mol. Biol. (rok: 2021, tom: 43, strony: 1374-1390), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/cimb43030098 - link to the publication
  7. More P450s Are Involved in Secondary Metabolite Biosynthesis in Streptomyces Compared to Bacillus, Cyanobacteria, and Mycobacterium
    Authors:
    Fanele Cabangile Mnguni, Tiara Padayachee, Wanping Chen, Dominik Gront, Jae-Hyuk Yu, David R. Nelson, and Khajamohiddin Syed
    Academic press:
    International Journal of Molecular Sciences (rok: 2020, tom: 21, strony: 4814), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms21134814 - link to the publication
  8. VisuaLife: library for interactive visualization in rich web applications
    Authors:
    Krys, JD Gront, D
    Academic press:
    Bioinformatics (rok: 2021, tom: 37, strony: 3662-3663), Wydawca: OXFORD UNIV PRESS
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btab251 - link to the publication
  9. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks
    Authors:
    Leman, Julia Koehler et al.
    Academic press:
    Nature Communications (rok: 2021, tom: 12, strony: 6947), Wydawca: NATURE RESEARCH
    Status:
    Published
    DOI:
    10.1038/s41467-021-27222-7 - link to the publication
  10. In Silico Structural Modeling and Analysis of Interactions of Tremellomycetes Cytochrome P450 Monooxygenases CYP51s with Substrates and Azoles
    Authors:
    Olufunmilayo Olukemi Akapo , Joanna M. Macnar , Justyna D. Kryś , Puleng Rosinah Syed , Khajamohiddin Syed and Dominik Gront
    Academic press:
    Int. J. Mol. Sci. (rok: 2021, tom: 22, strony: 7811), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms22157811 - link to the publication
  11. Lifestyles Shape the Cytochrome P450 Repertoire of the Bacterial Phylum Proteobacteria
    Authors:
    Siphesihle Msweli, Andiswa Chonco, Lihle Msweli, Puleng Rosinah Syed, Rajshekhar Karpoormath, Wanping Chen, Dominik Gront, Bridget Valeria Zinhle Nkosi, David R. Nelson, Khajamohiddin Syed
    Academic press:
    Int. J. Mol. Sci. (rok: 2022, tom: 23, strony: 5821), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms23105821 - link to the publication
  12. Coarse-grained potential for hydrogen bond interactions
    Authors:
    J. Kryś, D. Gront
    Academic press:
    Journal of Molecular Graphics and Modelling (rok: 2023, tom: 124, strony: 108507), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2023.108507 - link to the publication
  13. In Silico Analysis of P450s and Their Role in Secondary Metabolism in the Bacterial Class Gammaproteobacteria
    Authors:
    Ntombizethu Nokuphiwa Msomi, Tiara Padayachee, Nomfundo Nzuza, Puleng Rosinah Syed, Justyna Dorota Kryś , Wanping Chen, Dominik Gront , David R. Nelson , and Khajamohiddin Syed
    Academic press:
    Molecules (rok: 2021, tom: 26, strony: 1538), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/molecules26061538 - link to the publication
  14. Ancient Bacterial Class Alphaproteobacteria Cytochrome P450 Monooxygenases Can Be Found in Other Bacterial Species
    Authors:
    Nomfundo Nzuza 1, Tiara Padayachee, Puleng Rosinah Syed, Justyna Dorota Kryś , Wanping Chen, Dominik Gront , David R. Nelson and Khajamohiddin Syed
    Academic press:
    Int. J. Mol. Sci. (rok: 2021, tom: 22, strony: 5542), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms22115542 - link to the publication
  15. Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps
    Authors:
    D. Kim, D. Gront, K. Sanbonmatsu
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2020, tom: 60, strony: 2436–2442), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.0c00090 - link to the publication
  16. Better together: Elements of successful scientific software development in a distributed collaborative community
    Authors:
    J. Koehler Leman, B. Weitzner, P.D. Renfrew, S. Lewis, R. Moretti, A. Watkins, V. Mulligan, S. Lyskov, J. Adolf-Bryfogle, J. Labonte, J. Krys, C. Bystroff, W. Schief, D. Gront, O. Schueler-Furman, D. Baker, P. Bradley, R. Dunbrack, T. Kortemme, A. Leaver-Fay, C.M. Strauss, J. Meiler, B. Kuhlman, J. Gray, R. Bonneau
    Academic press:
    PLOS Computational Biology (rok: 2020, tom: 16, strony: e1007507), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pcbi.1007507 - link to the publication
  17. Macromolecular modeling and design in Rosetta: recent methods and frameworks
    Authors:
    nie mieszczą się w formularzu
    Academic press:
    Nature Methods (rok: 2020, tom: 17, strony: 665-680), Wydawca: Nature
    Status:
    Published
    DOI:
    10.1038/s41592-020-0848-2 - link to the publication

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