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Information of the project and the call

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Global protein docking algorithms based on the UNRES coarse-grained model

2015/17/N/ST4/03937

Keywords:

Molecular docking protein complexes

Descriptors:

  • ST4_15: Colloid chemistry
  • ST6_12: Scientific computing, simulation and modelling tools
  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation

Panel:

ST4 - Chemistry: physical chemistry/chemical physics, theoretical chemistry, analytical chemistry, inorganic chemistry, organic chemistry, method development

Host institution :

Uniwersytet Gdański, Wydział Chemii

woj. pomorskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Paweł Krupa 

Number of co-investigators in the project: 2

Call: PRELUDIUM 9 - announced on 2015-03-16

Amount awarded: 77 000 PLN

Project start date (Y-m-d): 2016-01-28

Project end date (Y-m-d): 2018-01-27

Project duration:: 24 months (the same as in the proposal)

Project status: Project settled

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.

Equipment purchased [PL]

  1. Nod komputerowy (1 362 PLN)
  2. Laptop (7 638 PLN)

Information in the final report

  • Publication in academic press/journals (8)
  • Book publications / chapters in book publications (2)
  1. Re-optimized UNRES Potential for Protein Model Quality Assessment
    Authors:
    E. Faraggi, P. Krupa, M.A. Mozolewska, A. Liwo, A. Kloczkowski
    Academic press:
    Genes (rok: 2018, tom: 9, strony: 601), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/genes9120601 - link to the publication
  2. Stability of α-Synuclein - Aβ42 Heterodimer: A Molecular Dynamics Study
    Authors:
    Yuliia Varenyk, Panagiotis E. Theodorakis, Dinh Q.H. Pham, Mai Suan Li, Paweł Krupa
    Academic press:
    PROTEINS: Structure, Function, and Bioinformatics , Wydawca: Wiley
    Status:
    Submitted
    DOI:
    brak - link to the publication
  3. Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information
    Authors:
    Agnieszka S. Karczyńska, Magdalena A. Mozolewska, Paweł Krupa, Artur Giełdoń, Adam Liwo, Cezary Czaplewski
    Academic press:
    Proteins: Structure, Function, and Bioinformatics (rok: 2018, tom: 86, strony: 228-239), Wydawca: Wiley Periodicals, Inc
    Status:
    Published
    DOI:
    10.1002/prot.25421 - link to the publication
  4. UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations
    Authors:
    Paweł Krupa, Agnieszka S. Karczyńska, Magdalena A. Mozolewska, Adam Liwo, Cezary Czaplewski
    Academic press:
    Bioinformatics (rok: 2021, ), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btaa897 - link to the publication
  5. Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: test with CASP12 targets
    Authors:
    Agnieszka Karczyńska, Magdalena A. Mozolewska, Paweł Krupa, Artur Giełdoń, Krzysztof K. Bojarski, Bartłomiej Zaborowski, Adam Liwo, Rafał Ślusarz, Magdalena Ślusarz, Jooyoung Lee, Keehyoung Joo, and Cezary Czaplewski
    Academic press:
    Journal of Molecular Graphics and Modelling (rok: 2018, tom: 83, strony: 92-99), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2018.05.008 - link to the publication
  6. Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment
    Authors:
    Marc F. Lensink*, Guillaume Brysbaert, Nurul Nadzirin, Sameer Velankar, Raphaël A.G. Chaleil, Tereza Gerguri, Paul A. Bates, Elodie Laine, Alessandra Carbone, Sergei Grudinin, Ren Kong, Ran-Ran Liu, Xi-Ming Xu, Hang Shi, Shan Chang, Miriam Eisenstein, Agnieszka Karczynska, Cezary Czaplewski, Emilia Lubecka, Agnieszka Lipska, Paweł Krupa, Magdalena Mozolewska, Łukasz Golon, Sergey Samsonov, Adam Liwo, Silvia Crivelli, Guillaume Pagès, Mikhail Karasikov, Maria Kadukova, Yumeng Yan, Sheng-You Huang, Mireia Rosell, Luis Angel Rodríguez-Lumbreras, Miguel Romero-Durana, Lucía Díaz-Bueno, Juan Fernandez-Recio, Charles Christoffer, Genki Terashi, Woong-Hee Shin, Tunde Aderinwale, Sai Raghavendra Maddhuri Venkata Subraman, Daisuke Kihara, Dima Kozakov, Sandor Vajda, Kathyn Porter, Dzmitry Padhorny, Israel Desta, Dmitri Beglov, Mikhail Ignatov, Sergey Kotelnikov, Iain H. Moal, David W. Ritchie, Isaure Chauvot de Beauchêne, Bernard Maigret, Marie-Dominique Devignes, Maria Elisa Ruiz Echartea, Didier Barradas-Bautista, Zhen Cao, Luigi Cavallo, Romina Oliva, Yue Cao, Yang Shen, Minkyung Baek, Taeyong Park, Hyeonuk Woo, Chaok Seok, Merav Braitbard, Lirane Bitton, Dina Scheidman-Duhovny, Justas Dapkūnas, Kliment Olechnovič, Česlovas Venclovas, Petras J. Kundrotas, Saveliy Belkin, Devlina Chakravarty, Varsha D. Badal, Ilya A. Vakser, Thom Vreven, Sweta Vangaveti, Tyler Borrman, Zhiping Weng, Johnathan D. Guest, Ragul Gowthaman, Brian G. Pierce, Xianjin Xu, Rui Duan, Liming Qiu, Jie Hou, Benjamin Ryan Merideth, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Panos I. Koukos, Jorge Roel-Touris, Francesco Ambrosetti, Cunliang Geng, Jörg Schaarschmidt, Mikael E. Trellet, Adrien S.J. Melquiond, Li Xue, Brian Jiménez-García, Charlotte W. van Noort, Rodrigo V. Honorato, Alexandre M.J.J. Bonvin, Shoshana J. Wodak
    Academic press:
    Proteins: Structure, Function, and Bioinformatics (rok: 2019, tom: 87, strony: 1200-1221), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/prot.25838 - link to the publication
  7. Performance of protein-structure predictions with the physics-based UNRES force field in CASP11
    Authors:
    P. Krupa, M.A. Mozolewska, M. Wiśniewska, Y. Yin, Y. He, A.K. Sieradzan, R. Ganzynkowicz, A.G. Lipska, A. Karczyńska, M. Ślusarz, R. Ślusarz, A. Giełdoń, C. Czaplewski, D. Jagieła, B. Zaborowski, H.A. Scheraga
    Academic press:
    Bioinformatics (rok: 2016, tom: 31, strony: 3270-3278), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btw404 - link to the publication
  8. Prediction of CD28-CD86 protein complex structure using different level of resolution approach
    Authors:
    Paweł Krupa, Marta Spodzieja, Adam K. Sieradzan
    Academic press:
    Journal of Molecular Graphics and Modelling (rok: 2021, tom: 103, strony: 0), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2020.107802 - link to the publication
  1. Physics-based coarse-grained modeling in bio- and nanochemistry
    Authors:
    Adam Liwo, Adam K. Sieradzan, Agnieszka S. Karczyńska, Emilia A. Lubecka, Sergey A. Samsonov, Cezary Czaplewski, Paweł Krupa, Magdalena Mozolewska
    Book:
    Practical Aspects of Computational Chemistry V , Wydawca: Springer
    Status:
    Submitted
  2. Modeling the structure, dynamics, and transformations of proteins with the UNRES force field
    Authors:
    Adam K. Sieradzan, Cezary Czaplewski, Paweł Krupa, Magdalena A. Mozolewska, Agnieszka Karczyńska, Agnieszka Lipska, Emilia A. Lubecka, Ewa Gołaś, Tomasz Wirecki, Mariusz Makowski, Stanisław Ołdziej, Adam Liwo
    Book:
    Methods in Molecular Biology (rok: 2018, ), Wydawca: Springer
    Status:
    Accepted for publication

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