Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Integrative methods for modeling protein-protein complexes and multimolecular assemblies

2021/40/Q/NZ2/00078

Keywords:

protein-protein docking coarse-grained modeling multiscale modeling molecular docking

Descriptors:

  • NZ2_010:
  • NZ2_007:
  • NZ2_008:

Panel:

NZ2 - Genetics, genomics: molecular genetics, genomics, proteomics, bioinformatics, systems biology, genetic epidemiology

Host institution :

Uniwersytet Warszawski, Centrum Nauk Biologiczno-Chemicznych

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Sebastian Kmiecik 

Number of co-investigators in the project: 6

Call: SHENG 2 - announced on 2020-12-15

Amount awarded: 1 918 816 PLN

Project start date (Y-m-d): 2021-12-22

Project end date (Y-m-d): 2025-12-21

Project duration:: 48 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 (9)
  1. A3DyDB: exploring structural aggregation propensities in the yeast proteome
    Authors:
    Javier Garcia-Pardo, Aleksandra E. Badaczewska-Dawid, Carlos Pintado-Grima, Valentín Iglesias, Aleksander Kuriata, Sebastian Kmiecik, Salvador Ventura
    Academic press:
    Microbial Cell Factories (rok: 2023, tom: 22, strony: 186), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12934-023-02182-3 - link to the publication
  2. Efficient improvement of the proliferation, differentiation, and anti-arthritic capacity of mesenchymal stem cells by simply culturing on the immobilized FGF2 derived peptide, 44-ERGVVSIKGV-53
    Authors:
    Soo Bin Lee, Ahmed Abdal Dayem, Sebastian Kmiecik, Kyung Min Lim, Dong Sik Seo, Hyeong-Taek Kim, Polash Kumar Biswas, Minjae Do, Deok-Ho Kim, Ssang-Goo Cho
    Academic press:
    Journal of Advanced Research (rok: 2023, tom: 28, strony: S2090-1232), Wydawca: Elsevier B.V.
    Status:
    Published
    DOI:
    10.1016/j.jare.2023.09.041 - link to the publication
  3. A3DyDB: exploring structural aggregation propensities in the yeast proteome
    Authors:
    Javier Garcia-Pardo, Aleksandra E. Badaczewska-Dawid, Carlos Pintado-Grima, Valentín Iglesias, Aleksander Kuriata, Sebastian Kmiecik, Salvador Ventura
    Academic press:
    Microbial Cell Factories (rok: 2023, tom: 22, strony: 186), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12934-023-02182-3 - link to the publication
  4. Fatty Acids Reverse the Supramolecular Chirality of Insulin Fibrils
    Authors:
    Aidan P Holman, Kimberly Quinn, Rakesh Kumar, Sebastian Kmiecik, Abid Ali, Dmitry Kurouski
    Academic press:
    The Journal of Physical Chemistry Letters (rok: 2023, tom: 14, 30, strony: 6935–6939), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jpclett.3c01527 - link to the publication
  5. Exploring protein functions from structural flexibility using CABS-flex modeling.
    Authors:
    Chandran Nithin, Rocco Peter Fornari, Smita P. Pilla, Karol Wroblewski, Mateusz Zalewski, Rafał Madaj, Andrzej Kolinski, Joanna M. Macnar, Sebastian Kmiecik
    Academic press:
    Protein Science (rok: 2024, tom: 33(9), strony: e5090), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/pro.5090 - link to the publication
  6. RNA-Puzzles Round V: blind predictions of 23 RNA structures
    Authors:
    Fan Bu, Yagoub Adam, Ryszard W. Adamiak, Maciej Antczak, Belisa Rebeca H. de Aquino, Nagendar Goud Badepally, Robert T. Batey, Eugene F. Baulin, Pawel Boinski, Michal J. Boniecki, Janusz M. Bujnicki, Kristy A. Carpenter, Jose Chacon, Shi-Jie Chen, Wah Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne K. Dawson, Frank DiMaio, Feng Ding, Anne-Catherine Dock-Bregeon, Nikolay V. Dokholyan, Ron O. Dror, Stanisław Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Amiri Farsani, Adrian R. Ferré-D'Amaré, Caleb Geniesse, George E. Ghanim, Horacio V. Guzman, Iris V. Hood, Lin Huang, Dharm Skandh Jain, Farhang Jaryani, Lei Jin, Astha Joshi, Masha Karelina, Jeffrey S. Kieft, Wipapat Kladwang, Sebastian Kmiecik, Deepak Koirala, Markus Kollmann, Rachael C. Kretsch, Mateusz Kurciński, Jun Li, Shuang Li, Marcin Magnus, BenoÎt Masquida, S. Naeim Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Hoang Duong Nguyen, Grigory Nikolaev, Chandran Nithin, Grace Nye, Iswarya P. N. Pandaranadar Jeyeram, Alberto Perez, Phillip Pham, Joseph A. Piccirilli, Smita Priyadarshini Pilla, Radosław Pluta, Simón Poblete, Almudena Ponce-Salvatierra, Mariusz Popenda, Lukasz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzynska, Congzhou Mike Sha, Filip Stefaniak, Zhaoming Su, Krishna C. Suddala, Marta Szachniuk, Raphael Townshend, Robert J. Trachman III, Jian Wang, Wenkai Wang, Andrew Watkins, Tomasz K. Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph David Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Zok, Dong Zhang, Sicheng Zhang, Adriana Żyła, Eric Westhof & Zhichao Miao
    Academic press:
    Nature Methods (rok: 2024, tom: 22, strony: 399–411), Wydawca: Springer nature
    Status:
    Published
    DOI:
    10.1038/s41592-024-02543-9 - link to the publication
  7. Aggrescan4D: Structure-informed analysis of pH-dependent protein aggregation
    Authors:
    Oriol Bárcenas, Aleksander Kuriata, Mateusz Zalewski, Valentín Iglesias, Carlos Pintado-Grima, Grzegorz Firlik, Michał Burdukiewicz, Sebastian Kmiecik, Salvador Ventura
    Academic press:
    Nucleic Acids Research (rok: 2024, tom: 52(W1), strony: W170–W175), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/nar/gkae382 - link to the publication
  8. Aggrescan4D: A comprehensive tool for pH-dependent analysis and engineering of protein aggregation propensity.
    Authors:
    Mateusz Zalewski, Valentin Iglesias, Oriol Bárcenas, Salvador Ventura, Sebastian Kmiecik
    Academic press:
    Protein Science (rok: 2024, tom: 33(10), strony: e5180), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/pro.5180 - link to the publication
  9. A3D Model Organism Database (A3D-MODB): a database for proteome aggregation predictions in model organisms
    Authors:
    Aleksandra E Badaczewska-Dawid, Aleksander Kuriata, Carlos Pintado-Grima, Javier Garcia-Pardo, Michał Burdukiewicz, Valentín Iglesias, Sebastian Kmiecik, Salvador Ventura
    Academic press:
    Nucleic Acids Research (rok: 2023, tom: 52, D1, strony: D360–D367), Wydawca: Oxford academic
    Status:
    Published
    DOI:
    10.1093/nar/gkad942 - link to the publication

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