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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

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 (6)
  1. RNA-Puzzles Round V: blind predictions of 23 RNA structures
    Authors:
    Fan Bu, Yagoub Adam, Ryszard Adamiak, Maciej Antczak, Belisa de Aquino, Nagendar Badepally, Robert Batey, Eugene Baulin, Pawel Boinski, Michal Boniecki, Janusz Bujnicki, Kristy Carpenter, Jose Chacon, Shi-Jie Chen, Wah Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne Dawson, Frank DiMaio, Feng Ding, Anne-Catherine Dock-Bregeon, Nikolay Dokholyan, Ron Dror, Stanislaw Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Farsani, Adrian Ferré-D'Amaré, Caleb Geniesse, George Ghanim, Horacio Guzman, Iris Hood, Lin Huang, Dharm Jain, Farhang Jaryani, Lei Jin, Astha Joshi, Masha Karelina, Jeffrey Kieft, Wipapat Kladwang, Sebastian Kmiecik, Deepak Koirala, Markus Kollmann, Rachael Kretsch, Mateusz Kurcinski, Shuang Li, Jun Li, Marcin Magnus, BenoÎt Masquida, Seyed Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Nguyen, Grigory Nikolaev, Chandran Nithin, Grace Nye, Iswarya Pandara Nayaka Pandaranadar Jeyeram, Alberto Perez, Phillip Pham, Joseph Piccirilli, Smita Pilla, Radoslaw Pluta, Simon Poblete, Almudena Ponce-Salvatierra, Lukasz Popenda, Mariusz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzynska, Congzhou Sha, Filip Stefaniak, Zhaoming Su, Krishna Suddala, Marta Szachniuk, Raphael Townshend, Robert Trachman III, Wenkai Wang, Jian Wang, Andrew Watkins, Tomasz Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Zok, Dong Zhang, Sicheng Zhang, Adriana Żyla, Eric Westhof, Zhichao Miao
    Academic press:
    Nature Methods (rok: 2025, tom: 22, strony: 399–411), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41592-024-02543-9 - link to the publication
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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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