Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

Keywords

Equipment

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New and efficient methods for the flexible molecular docking of proteins.

2014/14/A/ST6/00088

Keywords:

protein structure protein molecular docking protein interactions

Descriptors:

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

Panel:

ST6 - Computer science and informatics: informatics and information systems, computer science, scientific computing, intelligent systems

Host institution :

Uniwersytet Warszawski, Wydział Chemii

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Andrzej Koliński 

Number of co-investigators in the project: 10

Call: MAESTRO 6 - announced on 2014-06-16

Amount awarded: 3 285 600 PLN

Project start date (Y-m-d): 2015-05-25

Project end date (Y-m-d): 2021-01-24

Project duration:: 68 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Komputery osobiste (3 szt.) (24 000 PLN)
  2. Oprogramowanie (3 szt.) (2 250 PLN)

Information in the final report

  • Publication in academic press/journals (24)
  • Book publications / chapters in book publications (8)
  1. CABS-flex 2.0: a web server for fast simulations of flexibility of protein structures
    Authors:
    Aleksander Kuriata, Aleksandra Maria Gierut, Tymoteusz Oleniecki, Maciej Paweł Ciemny, Andrzej Kolinski, Mateusz Kurcinski, Sebastian Kmiecik
    Academic press:
    Nucleic Acids Research (rok: 2018, tom: 46, Issue W1, strony: W338–W343), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gky356 - link to the publication
  2. Coarse-Grained Modeling of the Interplay between Secondary Structure Propensities and Protein Fold Assembly
    Authors:
    Aleksandra E. Dawid, Dominik Gront and Andrzej Kolinski
    Academic press:
    Journal of Chemical Theory and Computation (rok: 2018, tom: 14, strony: 2277−2287), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.jctc.7b01242 - link to the publication
  3. Modeling of protein–peptide interactions using the CABS-dock web server for binding site search and flexible docking
    Authors:
    Maciej Blaszczyk, Mateusz Kurcinski, Maksim Kouza, Lukasz Wieteska, Aleksander Debinski, Andrzej Kolinski, Sebastian Kmiecik
    Academic press:
    Methods (rok: 2016, tom: 93, strony: 72-83), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.ymeth.2015.07.004 - link to the publication
  4. Role of Resultant Dipole Moment in Mechanical Dissociation of Biological Complexes
    Authors:
    Maksim Kouza, Anirban Banerji, Andrzej Kolinski, Irina Buhimschi and Andrzej Kloczkowski
    Academic press:
    Molecules (rok: 2018, tom: 23, strony: 1995), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/molecules23081995 - link to the publication
  5. Flexible docking of peptides to proteins using CABS-dock
    Authors:
    Mateusz Kurcinski, Aleksandra Badaczewska‐Dawid, Michal Kolinski, Andrzej Kolinski, Sebastian Kmiecik
    Academic press:
    Protein Science (rok: 2020, tom: 29, strony: 211-222), Wydawca: The Protein Society
    Status:
    Published
    DOI:
    10.1002/pro.3771 - link to the publication
  6. Protein secondary structure prediction using a small training set (compact model) combined with a Complex-valued neural network approach
    Authors:
    Shamima Rashid, Saras Saraswathi, Andrzej Kloczkowski, Suresh Sundaram and Andrzej Kolinski
    Academic press:
    BMC Bioinformatics (rok: 2016, tom: 17, strony: 362), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12859-016-1209-0 - link to the publication
  7. Protein–peptide docking using CABS-dock and contact information
    Authors:
    Maciej Blaszczyk, Maciej Pawel Ciemny, Andrzej Kolinski, Mateusz Kurcinski and Sebastian Kmiecik
    Academic press:
    Briefings in Bioinformatics (rok: 2018, tom: 20(6), strony: 2299-2305), Wydawca: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bib/bby080 - link to the publication
  8. A protocol for CABS-dock protein–peptide docking driven by side-chain contact information
    Authors:
    Mateusz Kurcinski, Maciej Blaszczyk, Maciej Pawel Ciemny, Andrzej Kolinski and Sebastian Kmiecik
    Academic press:
    BioMedical Engineering OnLine (rok: 2017, tom: 16(Suppl 1), strony: 73), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12938-017-0363-6 - link to the publication
  9. Aggrescan3D standalone package for structure-based prediction of protein aggregation properties.
    Authors:
    Kuriata Aleksander, Iglesias Valentin, Kurciński Mateusz , Ventura Salvador, Kmiecik Sebastian
    Academic press:
    Bioinformatics (rok: 2019, tom: 35(19), strony: 3834–3835), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btz143 - link to the publication
  10. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study
    Authors:
    Maksim Kouza, Nguyen Truong Co, Mai Suan Li, Sebastian Kmiecik, Andrzej Kolinski, Andrzej Kloczkowski, and Irina Alexandra Buhimschi
    Academic press:
    The Journal of Chemical Physics (rok: 2018, tom: 148, strony: 215106), Wydawca: AIP Publishing
    Status:
    Published
    DOI:
    10.1063/1.5028575 - link to the publication
  11. Oligomerization of FVFLM peptides and their ability to inhibit beta amyloid peptides aggregation: consideration as a possible model
    Authors:
    M. Kouza, A. Banerji, A. Kolinski, I. A. Buhimschi and A. Kloczkowski
    Academic press:
    Physical Chemistry Chemical Physics (rok: 2017, tom: 19, strony: 2990-2999), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/C6CP07145G - link to the publication
  12. Protein–Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations
    Authors:
    Mateusz Kurcinski, Sebastian Kmiecik, Mateusz Zalewski and Andrzej Kolinski
    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
  13. Protein–peptide docking: opportunities and challenges
    Authors:
    Maciej Ciemny, Mateusz Kurcinski, Karol Kamel, Andrzej Kolinski, Nawsad Alam, Ora Schueler-Furman and Sebastian Kmiecik
    Academic press:
    Drug Discovery Today (rok: 2018, tom: Vol. 23, No 8, strony: 1530-1537), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.drudis.2018.05.006 - link to the publication
  14. SURPASS Low-Resolution Coarse-Grained Protein Modeling
    Authors:
    Aleksandra E. Dawid, Dominik Gront, and Andrzej Kolinski
    Academic press:
    Journal of Chemical Theory and Computation (rok: 2017, tom: 13(11), strony: 5766–5779), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jctc.7b00642 - link to the publication
  15. Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields
    Authors:
    Maciej Pawel Ciemny, Aleksandra Elzbieta Badaczewska-Dawid, Monika Pikuzinska, Andrzej Kolinski and Sebastian Kmiecik
    Academic press:
    International Journal of Molecular Sciences (rok: 2019, tom: 20(3), strony: 606), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms20030606 - link to the publication
  16. Switch from thermal to force-driven pathways of protein refolding
    Authors:
    Maksim Kouza, Pham Dang Lan, Alexander M. Gabovich, Andrzej Kolinski, and Mai Suan Li
    Academic press:
    The Journal of Chemical Physics (rok: 2017, tom: 146, strony: 135101), Wydawca: American Institute of Physics
    Status:
    Published
    DOI:
    10.1063/1.4979201 - link to the publication
  17. Aggrescan3D (A3D) 2.0: prediction and engineering of protein solubility
    Authors:
    Kuriata Aleksander, Iglesias Valentin, Pujols Jordi, Kurciński Mateusz , Kmiecik Sebastian, Ventura Salvador
    Academic press:
    Nucleic Acids Research (rok: 2019, tom: 47 (W1), strony: W300–W307), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkz321 - link to the publication
  18. CABS-dock standalone: a toolbox for flexible protein-peptide docking
    Authors:
    Mateusz Kurcinski, Maciej Pawel Ciemny, Tymoteusz Oleniecki, Aleksander Kuriata, Aleksandra E Badaczewska-Dawid, Andrzej Kolinski, Sebastian Kmiecik
    Academic press:
    Bioinformatics (rok: 2019, tom: 35(20), strony: 4170-4172), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/btz185 - link to the publication
  19. CABS-flex standalone: a simulation environment for fast modeling of protein flexibility
    Authors:
    Mateusz Kurcinski, Tymoteusz Oleniecki, Maciej Pawel Ciemny, Aleksander Kuriata, Andrzej Kolinski and Sebastian Kmiecik
    Academic press:
    Bioinformatics (rok: 2018, tom: 35(4), strony: 694–695), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/bioinformatics/bty685 - link to the publication
  20. Coarse-grained protein models and their applications
    Authors:
    Sebastian Kmiecik, Dominik Gront, Michal Kolinski, Lukasz Wieteska, Aleksandra Dawid, Andrzej Koliński
    Academic press:
    Chemical Reviews (rok: 2016, tom: 116 (14), strony: 7898–7936), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.chemrev.6b00163 - link to the publication
  21. Computational reconstruction of atomistic protein structures from coarse-grained models
    Authors:
    Aleksandra E.Badaczewska-DawidAndrzejKolinskiSebastianKmiecik
    Academic press:
    Computational and Structural Biotechnology Journal (rok: 2020, tom: 18, strony: 162-176), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.csbj.2019.12.007 - link to the publication
  22. Modeling EphB4-EphrinB2 protein–protein interaction using flexible docking of a short linear motif
    Authors:
    Maciej Pawel Ciemny, Mateusz Kurcinski, Maciej Blaszczyk, Andrzej Kolinski and Sebastian Kmiecik
    Academic press:
    BioMedical Engineering OnLine (rok: 2017, tom: 16(Suppl 1), strony: 71), Wydawca: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12938-017-0362-7 - link to the publication
  23. Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models
    Authors:
    Sebastian Kmiecik, Maksim Kouza, Aleksandra E. Badaczewska-Dawid, Andrzej Kloczkowski and Andrzej Kolinski
    Academic press:
    Internationa Journal of Molecular Sciences (rok: 2018, tom: 19, strony: 3496), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/ijms19113496 - link to the publication
  24. Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction
    Authors:
    Maciej Ciemny, Aleksander Debinski, Marta Paczkowska, Andrzej Koliński, Mateusz Kurcinski, Sebastian Kmiecik
    Academic press:
    Scientific Reports (rok: 2016, tom: 6, strony: 37532), Wydawca: Macmillan Publishers Limited, part of Springer Nature
    Status:
    Published
    DOI:
    10.1038/srep37532 - link to the publication
  1. Fast and Accurate Accessible Surface Area Prediction Without a Sequence Profile
    Authors:
    Eshel Faraggi, Maksim Kouza, Yaoqi Zhou, and Andrzej Kloczkowski
    Book:
    Prediction of Protein Secondary Structure, Methods in Molecular Biology (rok: 2017, tom: vol. 1484, strony: 127-136), Wydawca: Springer Science+Business Media New York
    Status:
    Published
  2. Protein Dynamics Simulations Using Coarse- Grained Models"
    Authors:
    S. Kmiecik, J. Wabik, M. Kolinski, M. Kouza, A. Kolinski,
    Book:
    Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes - From Bioinformatics to Molecular Quantum Mechanics, Springer Series in Bio-Neuroinformatics (rok: 2019, tom: 8, strony: 61-87), Wydawca: Springer
    Status:
    Published
  3. One-Dimensional Structural Properties of Proteins in the Coarse-Grained CABS Model
    Authors:
    Sebastian KmiecikAndrzej Kolinski
    Book:
    Prediction of Protein Secondary Structure, Methods in Molecular Biology (rok: 2017, tom: vol. 1484, strony: 83-113), Wydawca: Springer Science+Business Media New York
    Status:
    Published
    DOI:
    link to the publication
  4. The GOR Method of Protein Secondary Structure Prediction and Its Application as a Protein Aggregation Prediction Tool
    Authors:
    Maksim Kouza, Eshel Faraggi, Andrzej Kolinski, Andrzej Kloczkowski
    Book:
    Prediction of Protein Secondary Structure, Methods in Molecular Biology (rok: 2017, tom: vol. 1484, strony: 45497), Wydawca: Springer Science+Business Media New York
    Status:
    Published
  5. Protein structure prediction using coarse-grained models
    Authors:
    M. Blaszczyk, D. Gront, S. Kmiecik, M. Kurcinski, M. Kolinski, M. P. Ciemny, K. Ziolkowska, M. Panek, A. Kolinski,
    Book:
    Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes - From Bioinformatics to Molecular Quantum Mechanics Springer Series on Bio- and Neurosystems (rok: 2019, tom: 8, strony: 27-59), Wydawca: Springer Nature Switzerland AG
    Status:
    Published
  6. Protocols for Fast Simulations of Protein Structure Flexibility Using CABS-Flex and SURPASS
    Authors:
    Aleksandra E Badaczewska-Dawid, Andrzej Kolinski, Sebastian Kmiecik
    Book:
    Protein Structure Prediction. Methods in Molecular Biology (rok: 2020, tom: 2165, strony: 337-353), Wydawca: Humana, New York, NY
    Status:
    Published
    DOI:
    link to the publication
  7. Explicit-Solvent All-atom Molecular Dynamics of Peptide Aggregation
    Authors:
    M. Kouza, A. Kolinski, I. A. Buhimschi, A. Kloczkowski,
    Book:
    Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes - From Bioinformatics to Molecular Quantum Mechanics, Springer Series in Bio-Neuroinformatics (rok: 2019, tom: 8, strony: 541-558), Wydawca: Springer
    Status:
    Published
  8. Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures
    Authors:
    Aleksandra E Badaczewska-Dawid, Alisa Khramushin, Andrzej Kolinski, Ora Schueler-Furman, Sebastian Kmiecik
    Book:
    Protein Structure Prediction. Methods in Molecular Biology (rok: 2020, tom: 2165, strony: 273-287), Wydawca: Humana, New York, NY
    Status:
    Published

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