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Information of the project and the call

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A framework for de novo modeling of RNA structures using restraints derived from experimental data

2021/43/D/NZ1/03360

Keywords:

RNA modeling X-ray crystallography cryoEM SAXS restraints SimRNA

Descriptors:

  • NZ1_004:
  • ST6_012:
  • ST6_013:

Panel:

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

Host institution :

Międzynarodowy Instytut Biologii Molekularnej i Komórkowej w Warszawie

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Sunandan Mukherjee 

Number of co-investigators in the project: 3

Call: SONATA 17 - announced on 2021-09-15

Amount awarded: 691 252 PLN

Project start date (Y-m-d): 2022-11-02

Project end date (Y-m-d): 2025-11-01

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

Project status: Pending project

Project description

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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 (5)
  1. 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, strony: 4), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btad527 - link to the publication
  2. MODOMICS: a database of RNA modifications and related information. 2023 update
    Authors:
    Andrea Cappannini, Angana Ray, Elżbieta Purta, Sunandan Mukherjee, Pietro Boccaletto, S Naeim Moafinejad, Antony Lechner, Charles Barchet, Bruno P Klaholz, Filip Stefaniak, Janusz M Bujnicki
    Academic press:
    Nucleic Acids Research (rok: 2023, tom: 52, strony: 5), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkad1083 - 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: Structure, Function, and Bioinformatics (rok: 2023, tom: 91, strony: 1800-1810), Wydawca: Wiley Online Library
    Status:
    Published
    DOI:
    10.1002/prot.26575 - link to the publication
  4. Structural basis of sRNA RsmZ regulation of Pseudomonas aeruginosa virulence
    Authors:
    Xinyu Jia, Zhiling Pan, Yang Yuan, Bingnan Luo, Yongbo Luo, Sunandan Mukherjee, Guowen Jia, Liu Liu, Xiaobin Ling, Xiting Yang, Zhichao Miao, Xiawei Wei, Janusz M Bujnicki, Kelei Zhao, Zhaoming Su
    Academic press:
    Cell Research (rok: 2023, tom: 33, strony: 3), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41422-023-00786-3 - link to the publication
  5. Conserved structures and dynamics in 5′-proximal regions of Betacoronavirus RNA genomes
    Authors:
    Tales Rocha de Moura, Elżbieta Purta, Agata Bernat, Eva M Martín-Cuevas, Małgorzata Kurkowska, Eugene F Baulin, Sunandan Mukherjee, Jakub Nowak, Artur P Biela, Michał Rawski, Sebastian Glatt, Fernando Moreno-Herrero, Janusz M Bujnicki
    Academic press:
    Nucleic Acids Research (rok: 2024, tom: Online ahead of print, strony: 1–14), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkae144 - link to the publication

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