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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Development of tools for the rational design of peptide therapeutics

2020/39/B/NZ2/01301

Keywords:

drug design structural bioinformatics protein-peptide docking coarse-grained modeling multiscale modeling

Descriptors:

  • NZ2_010:
  • NZ2_008:
  • NZ2_007:

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: OPUS 20 - announced on 2020-09-15

Amount awarded: 1 867 576 PLN

Project start date (Y-m-d): 2021-07-07

Project end date (Y-m-d): 2025-07-06

Project duration:: 48 months (the same as in the proposal)

Project status: Project completed

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 (11)
  1. 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
  2. Comparative analysis of RNA 3D structure prediction methods: towards enhanced modeling of RNA–ligand interactions
    Authors:
    Nithin C., Kmiecik S., Błaszczyk R., Nowicka J., Tuszyńska I.
    Academic press:
    Nucleic Acids Research (rok: 2024, tom: 52(13), strony: 7465-7486), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/nar/gkae541 - link to the publication
  3. A3D database: structure-based predictions of protein aggregation for the human proteome
    Authors:
    Badaczewska-Dawid A.E., Garcia-Pardo J.,Kuriata A., Pujols J., Ventura S., Kmiecik S.
    Academic press:
    Biorxiv (rok: 2021, tom: -, strony: -), Wydawca: -
    Status:
    Published
    DOI:
    10.1101/2021.11.17.468872 - link to the publication
  4. MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes.
    Authors:
    Badaczewska-Dawid A.E., Chandran N., Wróblewski K., Kurcinski M, Kmiecik S.
    Academic press:
    Nucleic Acids Research (rok: 2022, tom: 50, strony: W474–W482), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkac307 - link to the publication
  5. Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations
    Authors:
    Kurcinski, M.; Kmiecik, S.; Zalewski, M.; Kolinski, A.
    Academic press:
    International Journal of Molecular Sciences (rok: 2021, tom: 22, strony: 7341), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms22147341 - link to the publication
  6. Structure prediction of linear and cyclic peptides using CABS-flex
    Authors:
    Aleksandra Badaczewska-Dawid, Karol Wróblewski, Mateusz Kurcinski, Sebastian Kmiecik
    Academic press:
    Briefings in bioinformatics (rok: 2024, tom: 25, 2, strony: 45665), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bib/bbae003 - link to the publication
  7. Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations
    Authors:
    Kurcinski, M.; Kmiecik, S.; Zalewski, M.; Kolinski, A.
    Academic press:
    International Journal of Molecular Sciences (rok: 2021, tom: 22, strony: 7341), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms22147341 - link to the publication
  8. Structure prediction of linear and cyclic peptides using CABS-flex
    Authors:
    Aleksandra Badaczewska-Dawid, Karol Wróblewski, Mateusz Kurcinski, Sebastian Kmiecik
    Academic press:
    Briefings in bioinformatics (rok: 2024, tom: 25, 2, strony: 45665), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bib/bbae003 - link to the publication
  9. Integrating AlphaFold pLDDT Scores into CABS-flex for enhanced protein flexibility simulations.
    Authors:
    Karol Wróblewski , Sebastian Kmiecik
    Academic press:
    Computational and Structural Biotechnology Journal (rok: 2024, tom: 23, strony: 4350-4356), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.csbj.2024.11.047 - link to the publication
  10. 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, strony: e5090), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/pro.5090 - link to the publication
  11. MAPIYA contact map server for identification and visualization of molecular interactions in proteins and biological complexes.
    Authors:
    Badaczewska-Dawid A.E., Chandran N., Wróblewski K., Kurcinski M, Kmiecik S.
    Academic press:
    Nucleic Acids Research (rok: 2022, tom: 50, strony: W474–W482), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkac307 - link to the publication

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