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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Integrative modeling and structure determination of macromolecular complexes comprising RNA and proteins

2017/26/A/NZ1/01083

Keywords:

structural biology RNP molecular modeling docking crystallography SAXS electron microscopy

Descriptors:

  • NZ2_10: Biological systems analysis, modelling and simulation
  • NZ2_7: Bioinformatics
  • NZ1_4: Structural biology

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):

prof. Janusz Bujnicki 

Number of co-investigators in the project: 8

Call: MAESTRO 9 - announced on 2017-06-14

Amount awarded: 3 500 000 PLN

Project start date (Y-m-d): 2018-10-02

Project end date (Y-m-d): 2025-06-01

Project duration:: 60 months (the same as in the proposal)

Project status: Pending project

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.

Information in the final report

  • Publication in academic press/journals (12)
  • Book publications / chapters in book publications (2)
  1. 1D2DSimScore: A novel method for comparing contacts in biomacromolecules and their complexes
    Authors:
    S. Naeim Moafineja, Iswarya P. N. Pandaranadar Jeyeram, Farhang Jaryani, Niloofar Shirvanizadeh, Eugene F. Bauli, Janusz M. Bujnicki
    Academic press:
    Protein Science (rok: 2022, tom: 32, strony: 14), Wydawca: Wiley-Blackwell
    Status:
    Published
    DOI:
    10.1002/pro.4503 - link to the publication
  2. Computational modeling of RNA 3D structure based on experimental data
    Authors:
    Ponce-Salvatierra A+, Astha+, Merdas K+, Nithin C, Ghosh P, Mukherjee S and Bujnicki JM
    Academic press:
    Bioscience Reports (rok: 2019, tom: 39, strony: 45316), Wydawca: Portland Press (Biochemical Society)
    Status:
    Published
    DOI:
    10.1042/BSR20180430 - link to the publication
  3. RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints
    Authors:
    Eugene F. Baulin, Sunandan Mukherjee, S. Naeim Moafinejad, Tomasz K. Wirecki, Nagendar Goud Badepally, Farhang Jaryani, Filip Stefaniak, Masoud Amiri Farsani, Angana Ray, Tales Rocha de Moura, Janusz M. Bujnicki
    Academic press:
    Proteins (rok: 2023, tom: 91, strony: 1800-1810), Wydawca: Wiley Periodicals LLC
    Status:
    Published
    DOI:
    10.1002/prot.26575 - link to the publication
  4. Bioinformatics tools and benchmarks for computational docking and 3D structure prediction of RNA-protein complexes
    Authors:
    Nithin C, Ghosh P and Bujnicki JM
    Academic press:
    Genes (rok: 2018, tom: 9, strony: 432), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/genes9090432 - link to the publication
  5. Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements
    Authors:
    Manfredonia I, Nithin C, Ponce-Salvatierra MA, Ghosh P, Wirecki TK, Marinus T, Ogando NS, Eric J. Snijder EJ, van Hemert MJ, Bujnicki JM, Incarnato D
    Academic press:
    Nucleic Acids Research (rok: 2020, tom: Vol. 48, No. 22, strony: 12436–12452), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkaa1053 - link to the publication
  6. QRNAS: software tool for refinement of nucleic acid structures
    Authors:
    Stasiewicz J, Mukherjee S, Nithin C and Bujnicki JM
    Academic press:
    BMC Structural Biology (rok: 2019, tom: 19, strony: 45302), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12900-019-0103-1 - link to the publication
  7. RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints
    Authors:
    Grzegorz Chojnowski, Rafał Zaborowski, Marcin Magnus, Sunandan Mukherjee, Janusz M. Bujnicki
    Academic press:
    Bioinformatics (rok: 2023, tom: 39(9), strony: 45295), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad527 - link to the publication
  8. RNA target highlights in CASP15: Evaluation of predicted models by structure providers
    Authors:
    Kretsch RC, Andersen ES, Bujnicki JM, Chiu W, Das R, Luo B, Masquida B, McRae EKS, Schroeder GM, Su Z, Wedekind JE, Xu L, Zhang K, Zheludev IN, Moult J, Kryshtafovych A
    Academic press:
    Proteins: Structure, Function, and Bioinformatics (rok: 2023, tom: 91, strony: 1600-1615), Wydawca: Wiley Periodicals LLC
    Status:
    Published
    DOI:
    10.1002/prot.26550 - link to the publication
  9. Open Access Molecular insights into RNA recognition and gene regulation by the TRIM-NHL protein Mei-P26
    Authors:
    Anna Salerno-Kochan, Andreas Horn, Pritha Ghosh, Chandran Nithin, Anna Kościelniak, Andreas Meindl, Daniela Strauss, Rościsław Krutyhołowa, Oliver Rossbach, Janusz M.Bujnicki, Monika Gaik, Jan Medenbach, Sebastian Glatt
    Academic press:
    Life Science Alliance (rok: 2022, tom: 5, strony: e202201418), Wydawca: EMBO Press
    Status:
    Published
    DOI:
    10.26508/lsa.202201418 - link to the publication
  10. RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools
    Authors:
    Magnus M, Antczak M, Zok T, Wiedemann J, Lukasiak P, Cao Y, Bujnicki JM, Westhof E, Szachniuk M, Miao M
    Academic press:
    Nucleic Acids Research (rok: 2019, tom: Vol. 48, No. 2, strony: 576–588), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkz1108 - link to the publication
  11. Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence
    Authors:
    Jia X, Pan Z, Yuan Y, Luo B, Luo Y, Mukherjee S, Jia G, Liu L, Ling X, Yang X, Miao Z, Wei X, Bujnicki JM, Zhao K, Su Z
    Academic press:
    Cell Research (rok: 2023, tom: 33, strony: 328-330), Wydawca: Springernature
    Status:
    Published
    DOI:
    10.1038/s41422-023-00786-3 - link to the publication
  12. Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing
    Authors:
    Luo B, Zhang C, Ling X, Mukherjee S, Jia G, Xie J, Jia X, Liu L, Baulin EF, Luo Y, Jiang L, Dong H, Wei X, Bujnicki JM, Su Z
    Academic press:
    Nature Catalysis (rok: 2023, tom: 6 (4), strony: 298–309), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41929-023-00934-3 - link to the publication
  1. Modeling of three-dimensional RNA structures using SimRNA
    Authors:
    Wirecki TK, Nithin C, Mukherjee S, Bujnicki JM, Bonieck MJ
    Book:
    Protein Structure Prediction (4th edition) (rok: 2020, tom: NA, strony: NA), Wydawca: Springer
    Status:
    Published
  2. Computational modeling methods for 3D structure prediction of ribozymes
    Authors:
    Ghosh P, Nithin C, Astha, Stefaniak F, Wirecki TK, Bujnick JM
    Book:
    Ribozymes (rok: 2020, tom: NA, strony: NA), Wydawca: Wiley-VCH
    Status:
    Published

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