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Information on the principal investigator and host institution

Information of the project and the call

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An integrated approach to the prediction of the structures of proteins and protein complexes with the use of the coarse-grained UNRES force field and utilizing the information from structural data bases

2013/10/M/ST4/00640

Keywords:

protein structure prediction coarse-grained force fields template-based modeling molecular dynamics global optimization methods

Descriptors:

  • ST4_15: Colloid chemistry
  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation
  • NZ1_4: Structural biology

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):

prof. Józef Liwo 

Number of co-investigators in the project: 11

Call: HARMONIA 5 - announced on 2013-06-14

Amount awarded: 694 678 PLN

Project start date (Y-m-d): 2014-04-24

Project end date (Y-m-d): 2017-10-23

Project duration:: 42 months (the same as in the proposal)

Project status: Project settled

Information in the final report

  • Publication in academic press/journals (9)
  • Book publications / chapters in book publications (1)
  1. 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. Karczyńnska, 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
    Status:
    Published
    DOI:
    10.1002/prot.25421 - link to the publication
  2. Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins
    Authors:
    Agnieszka S. Karczyńska, Cezary Czaplewski, Paweł Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, and Adam Liwo
    Academic press:
    Journal of Computational Chemistry (rok: 2017, tom: 38, strony: 2730-2746), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/jcc.25070 - link to the publication
  3. Maximum likelihood calibration of the UNRES force field for simulation of protein structure and dynamics
    Authors:
    Paweł Krupa, Anna Hałabis, Wioletta Żmudzińska, Stanisław Ołdziej, Harold A. Scheraga, Adam Liwo
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2017, tom: 57, strony: 2364-2377), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.7b00254 - link to the publication
  4. An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
    Authors:
    Chen Keasar, Liam J. McGuffin, Björn Wallner, Gaurav Chopra, Badri Adhikari, Debswapna Bhattacharya, Lauren Blake, Leandro Oliveira Bortot, Renzhi Cao, B.K. Dhanasekaran, Itzhel Dimas, Rodrigo Antonio Faccioli, Eshel Faraggi, Robert Ganzynkowicz, Sambit Ghosh, Soma Ghosh, Artur Giełdoń, Lukasz Golon, Yi He, Lim Heo, Jie Hou, Main Khan, Firas Khatib, George A. Khoury, Chris Kieslich, David E. Kim, Pawel Krupa, Gyu Rie Lee, Hongbo Li, Jilong Li, Agnieszka Lipska, Adam Liwo, Ali Hassan A. Maghrabi, Milot Mirdita, Shokoufeh Mirzaei, Magdalena A. Mozolewska, Melis Onel, Sergei Ovchinnikov, Anand Shah, Utkarsh Shah, Tomer Sidi, Adam K. Sieradzan, Magdalena Ślusarz, Rafal Ślusarz, James Smadbeck, Phanourios Tamamis, Nicholas Trieber, Tomasz Wirecki, Yanping Yin, Yang Zhang, Jaume Bacardit, Maciej Baranowski, Nicholas Chapman, Seth Cooper, Alexandre Defelicibus, Jeff Flatten, Brian Koepnick, Zoran Popović, Bartlomiej Zaborowski, David Baker, Jianlin Cheng, Cezary Czaplewski, Alexandre Cláudio Botazzo Delbem, Christodoulos Floudas, Andrzej Kloczkowski, Stanislaw Ołdziej, Michael Levitt, Harold Scheraga, Chaok Seok, Johannes Söding, Saraswathi Vishveshwara, Dong Xu, Foldit Players, Silvia N. Crivelli
    Academic press:
    Scientific Reports (rok: 2018, tom: 8, strony: 9939-1 - 9939-18), Wydawca: Nature Publishing Group
    Status:
    Published
    DOI:
    10.1038/s41598-018-26812-8 - link to the publication
  5. Reoptimized UNRES Potential for Protein Model Quality Assessment
    Authors:
    Eshel Faraggi, Pawel Krupa, Magdalena A. Mozolewska, Adam Liwo, Andrzej Kloczkowski
    Academic press:
    Genes (rok: 2018, tom: 9, strony: 601-1 - 601-17), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/genes9120601 - link to the publication
  6. Prediction of protein structure by template-based modeling combined with the UNRES force field
    Authors:
    Paweł Krupa, Magdalena A. Mozolewska, Keehyoung Joo, Jooyoung Lee, Cezary Czaplewski, Adam Liwo
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2015, tom: 55, strony: 1271-1281), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.5b00117 - link to the publication
  7. Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field
    Authors:
    Magdalena A. Mozolewska, Paweł Krupa, Bartłomiej Zaborowski, Adam Liwo, Jooyoung Lee, Keehyoung Joo, Cezary Czaplewski
    Academic press:
    Journal of Chemical Iinformation and Modeling (rok: 2016, tom: 56, strony: 2263-2279), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.6b00189 - link to the publication
  8. Use of the UNRES force field in template-assisted prediction of proteins 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:
    J. Mol. Graph. Model. (rok: 2018, tom: 83, strony: 92-99), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.jmgm.2018.05.008 - link to the publication
  9. In situ data analytics and indexing of protein trajectories
    Authors:
    Travis Johnston, Boyu Zhang, Adam Liwo, Silvia Crivelli, Michela Taufer
    Academic press:
    Journal of Computational Chemistry (rok: 2017, tom: 38, strony: 1419-1430), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/jcc.24729 - link to the publication
  1. Chemoinformatics Methods for Studying Biomolecules
    Authors:
    Adam Liwo, Cezary Czaplewski, Stanisław Ołdziej, Bartłomiej Zaborowski, Dawid Jagieła, Jooyoung Lee
    Book:
    Handbook of Computational Chemistry (rok: 2017, tom: 5, strony: 2183-2199), Wydawca: Springer International Publishing Switzerland
    Status:
    Published
    DOI:
    link to the publication

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