Projects funded by the NCN

Information on the principal investigator and host institution

Information of the project and the call

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Combination of Molecular Simulation and Deep Learning for De Novo Drug Design

2020/37/N/ST6/02728

Keywords:

deep learning neural networks computer aided drug design generative models molecular docking

Descriptors:

  • ST6_7: Artificial intelligence, intelligent systems, multi-agent systems
  • ST6_11: Machine learning, statistical data processing and applications using signal processing (e.g. speech, image, video)
  • 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 Jagielloński, Wydział Matematyki i Informatyki

woj.

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr Tomasz Jakub Danel 

Number of co-investigators in the project: 2

Call: PRELUDIUM 19 - announced on 2020-03-16

Amount awarded: 85 932 PLN

Project start date (Y-m-d): 2021-02-01

Project end date (Y-m-d): 2024-01-31

Project duration:: 36 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.

Information in the final report

  • Publication in academic press/journals (11)
  • Articles in post-conference publications (9)
  1. Generative Models Should at Least Be Able to Design Molecules That Dock Well: A New Benchmark
    Authors:
    Tobiasz Ciepliński, Tomasz Danel, Sabina Podlewska, Stanisław Jastrzębski
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2023, tom: 63, strony: 3238–3247), Wydawca: American Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.2c01355 - link to the publication
  2. Extended study on atomic featurization in graph neural networks for molecular property prediction
    Authors:
    Agnieszka Wojtuch, Tomasz Danel, Sabina Podlewska, Łukasz Maziarka
    Academic press:
    Journal of Cheminformatics (rok: 2024, tom: 15, strony: -), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s13321-023-00751-7 - link to the publication
  3. MedChem Game: Gamification of Drug Design
    Authors:
    Tomasz Danel, Jan Łęski, Sabina Podlewska, Igor T. Podolak
    Academic press:
    Journal of Chemical Education (rok: 2024, tom: nie dotyczy, strony: nie dotyczy), Wydawca: American Chemical Society
    Status:
    Submitted
  4. Docking-based generative approaches in the search for new drug candidates
    Authors:
    Tomasz Danel, Jan Łęski, Sabina Podlewska, Igor T Podolak
    Academic press:
    Drug Discovery Today (rok: 2023, tom: 28, strony: -), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.drudis.2022.103439 - link to the publication
  5. Relative molecule self-attention transformer
    Authors:
    Łukasz Maziarka, Dawid Majchrowski, Tomasz Danel, Piotr Gaiński, Jacek Tabor, Igor Podolak, Paweł Morkisz, Stanisław Jastrzębski
    Academic press:
    Journal of Cheminformatics (rok: 2024, tom: 16, strony: -), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s13321-023-00789-7 - link to the publication
  6. Docking-based generative approaches in the search for new drug candidates
    Authors:
    Tomasz Danel, Jan Łęski, Sabina Podlewska, Igor T Podolak
    Academic press:
    Drug Discovery Today (rok: 2023, tom: 28, strony: -), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.drudis.2022.103439 - link to the publication
  7. SONG: Self-Organizing Neural Graphs
    Authors:
    Łukasz Struski, Tomasz Danel, Marek Śmieja, Jacek Tabor, Bartosz Zieliński
    Academic press:
    Transactions on Pattern Analysis and Machine Intelligence
    Status:
    Submitted
  8. Generation of new inhibitors of selected cytochrome P450 subtypes – in silico study
    Authors:
    Tomasz Danel, Agnieszka Wojtuch, Sabina Podlewska
    Academic press:
    Computational and Structural Biotechnology Journal (rok: 2022, tom: 20, strony: 5639-5651), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.005 - link to the publication
  9. Generation of new inhibitors of selected cytochrome P450 subtypes – in silico study
    Authors:
    Tomasz Danel, Agnieszka Wojtuch, Sabina Podlewska
    Academic press:
    Computational and Structural Biotechnology Journal (rok: 2022, tom: 20, strony: 5639-5651), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.005 - link to the publication
  10. SONG: Self-Organizing Neural Graphs
    Authors:
    Łukasz Struski, Tomasz Danel, Marek Śmieja, Jacek Tabor, Bartosz Zieliński
    Academic press:
    Transactions on Pattern Analysis and Machine Intelligence
    Status:
    Submitted
  11. Machine learning accelerates pharmacophore-based virtual screening of MAO inhibitors
    Authors:
    Marcin Cieślak, Tomasz Danel, Olga Krzysztyńska-Kuleta, Justyna Kalinowska-Tłuścik
    Academic press:
    Scientific Reports (rok: 2024, tom: 14, strony: nie dotyczy), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1038/s41598-024-58122-7 - link to the publication
  1. ProGReST: Prototypical Graph Regression Soft Trees for Molecular Property Prediction
    Authors:
    Dawid Rymarczyk, Daniel Dobrowolski, Tomasz Danel
    Conference:
    Proceedings of the 2023 SIAM International Conference on Data Mining (SDM) (rok: 2023, tom: SIAM International Conference on Data Mining (SDM23), strony: 379 - 387), Wydawca: Society for Industrial and Applied Mathematics
    Data:
    konferencja 27-29 kwietnia 2023
    Status:
    Published
    DOI:
    10.1137/1.9781611977653.ch43 - link to the publication
  2. ProGReST: Prototypical Graph Regression Soft Trees for Molecular Property Prediction
    Authors:
    Dawid Rymarczyk, Daniel Dobrowolski, Tomasz Danel
    Conference:
    Proceedings of the 2023 SIAM International Conference on Data Mining (SDM) (rok: 2023, tom: SIAM International Conference on Data Mining (SDM23), strony: -), Wydawca: Society for Industrial and Applied Mathematics
    Data:
    konferencja 27-29 kwietnia 2023
    Status:
    Accepted for publication
  3. DrugGame: Gamification of Drug Design
    Authors:
    Tomasz Danel, Jan Łęski, Sabina Podlewska, Igor T. Podolak
    Conference:
    2022 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS) (tom: IROS 2022, strony: )
    Status:
    Submitted
  4. SONGs: Self-Organizing Neural Graphs
    Authors:
    Łukasz Struski, Tomasz Danel, Marek Śmieja, Jacek Tabor, Bartosz Zieliński
    Conference:
    2023 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV) (rok: 2023, tom: 2023 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), strony: 3837-3846), Wydawca: IEEE
    Data:
    konferencja 2-7 stycznia 2023
    Status:
    Published
    DOI:
    10.1109/WACV56688.2023.00384 - link to the publication
  5. DrugGame: Gamification of Drug Design
    Authors:
    Tomasz Danel, Jan Łęski, Sabina Podlewska, Igor T. Podolak
    Conference:
    2022 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS) (tom: IROS 2022, strony: )
    Status:
    Submitted
  6. Comparison of Atom Representations in Graph Neural Networks for Molecular Property Prediction
    Authors:
    Agnieszka Pocha, Tomasz Danel, Sabina Podlewska, Jacek Tabor, Łukasz Maziarka
    Conference:
    2021 International Joint Conference on Neural Networks (IJCNN) Proceedings (rok: 2021, tom: IJCNN 2021, strony: ), Wydawca: IEEE
    Data:
    konferencja 18-22 Lipca 2021
    Status:
    Published
    DOI:
    10.1109/IJCNN52387.2021.9533698 - link to the publication
  7. Comparison of Atom Representations in Graph Neural Networks for Molecular Property Prediction
    Authors:
    Agnieszka Pocha, Tomasz Danel, Sabina Podlewska, Jacek Tabor, Łukasz Maziarka
    Conference:
    2021 International Joint Conference on Neural Networks (IJCNN) Proceedings (rok: 2021, tom: IJCNN 2021, strony: ), Wydawca: IEEE
    Data:
    konferencja 18-22 Lipca 2021
    Status:
    Published
    DOI:
    10.1109/IJCNN52387.2021.9533698 - link to the publication
  8. Comparison of Atom Representations in Graph Neural Networks for Molecular Property Prediction
    Authors:
    Agnieszka Pocha, Tomasz Danel, Sabina Podlewska, Jacek Tabor, Łukasz Maziarka
    Conference:
    2021 International Joint Conference on Neural Networks (IJCNN) Proceedings (rok: 2021, tom: IJCNN 2021, strony: ), Wydawca: IEEE
    Data:
    konferencja 18-22 Lipca 2021
    Status:
    Published
    DOI:
    10.1109/IJCNN52387.2021.9533698 - link to the publication
  9. SONGs: Self-Organizing Neural Graphs
    Authors:
    Łukasz Struski, Tomasz Danel, Marek Śmieja, Jacek Tabor, Bartosz Zieliński
    Conference:
    2023 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV) (rok: 2023, tom: 2023 IEEE/CVF Winter Conference on Applications of Computer Vision (WACV), strony: 3837-3846), Wydawca: IEEE
    Data:
    konferencja 2-7 stycznia 2023
    Status:
    Published
    DOI:
    10.1109/WACV56688.2023.00384 - link to the publication

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