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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Development of a comprehensive set of computational tools for the search of new ligands of particular receptor - case study of 5-HT7R

2018/31/B/NZ2/00165

Keywords:

machine learning cheminformatics computer-aided drug design virtual screening

Descriptors:

  • NZ2_7: Bioinformatics
  • NZ7_14: Pharmacy, pharmacotherapy, pharmacology
  • ST6_13: Bioinformatics, biocomputing, DNA and molecular computation

Panel:

NZ2 - Genetics, genomics: molecular genetics, genomics, proteomics, bioinformatics, systems biology, genetic epidemiology

Host institution :

Instytut Farmakologii im. Jerzego Maja Polskiej Akademii Nauk

woj. małopolskie

Other projects carried out by the institution 

Principal investigator (from the host institution):

dr hab. Sabina Podlewska 

Number of co-investigators in the project: 4

Call: OPUS 16 - announced on 2018-09-14

Amount awarded: 645 200 PLN

Project start date (Y-m-d): 2019-11-26

Project end date (Y-m-d): 2023-11-25

Project duration:: 48 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. laptop (2 szt.) (10 000 PLN)
  2. komputer stacjonarny (9 569 PLN)
  3. oprogramowanie do modelowania molekularnego (9 600 PLN)

Information in the final report

  • Publication in academic press/journals (6)
  • Articles in post-conference publications (11)
  • Book publications / chapters in book publications (1)
  1. From data to knowledge:– systematic review of tools for automatic analysis of molecular dynamics output
    Authors:
    Baltrukevich, H.; Podlewska, S.
    Academic press:
    Frontiers in Pharmacology (rok: 2022, tom: 13, strony: 844293), Wydawca: Frontiers
    Status:
    Published
    DOI:
    10.3389/fphar.2022.844293 - link to the publication
  2. ADMET-PrInt: Evaluation of ADMET properties – prediction and interpretation
    Authors:
    Jamrozik, E.; Śmieja, M.; Podlewska, S.
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2024, ), Wydawca: American Chemical Society
    Status:
    Accepted for publication
    DOI:
    brak - link to the publication
  3. SERIFS: design of target-focused libraries by exploring active ligand subspaces encoded with fingerprints
    Authors:
    Rybka, H.; Iwan, M.; Siomchen, A.; Danel, T.; Podlewska, S.
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2023, ), Wydawca: American Chemical Society
    Status:
    Submitted
    DOI:
    brak - link to the publication
  4. Emulating Docking Results Using a Deep Neural Network: A New Perspective for Virtual Screening
    Authors:
    Jastrzębski, S.; Szymczak, M.; Pocha, A.; Mordalski, S.; Tabor, J.; Bojarski, A.J.; Podlewska, S.
    Academic press:
    Journal of Chemical Information and Modeling (rok: 2020, tom: 60, strony: 4246-4262), Wydawca: Americal Chemical Society
    Status:
    Published
    DOI:
    10.1021/acs.jcim.9b01202 - link to the publication
  5. Generation of new inhibitors of selected cytochrome P450 subtypes– in silico study
    Authors:
    Danel, T.; Wojtuch, A.; Podlewska, S.
    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
  6. Prediction of probability distributions of molecular properties – towards more efficient virtual screening and better understanding of compound representations
    Authors:
    Duda, J.; Podlewska, S.
    Academic press:
    Molecular Diversity (rok: 2022, tom: in press, strony: in press), Wydawca: Springer
    Status:
    Published
    DOI:
    10.1007/s11030-022-10589-0 - link to the publication
  1. Optimization of ADMET properties – ligand- and structure-based approach
    Authors:
    Kafel, R.; Podlewska, S.
    Conference:
    7th International Electronic Conference on Medicinal Chemistry (rok: 2021, ), Wydawca: MDPI
    Data:
    konferencja 2021-11-01-2021-11-30
    Status:
    Published
  2. Each answer has to be justified - a machine-learning based platform for evaluation of compound ADMET properties with explainability module
    Authors:
    Jamrozik, E.; Śmieja, M.; Podlewska, S.
    Conference:
    5th Central European Biomedical Congress 'Future trends in health interventions' (rok: 2023, ), Wydawca: Maj Institute of Pharmacology Polish Academy of Sciences
    Data:
    konferencja 2023-05-29-2023-06-01
    Status:
    Published
  3. Detection of structural features influencing compound physicochemical properties with the use of SHAP values
    Authors:
    Pocha, A.; Jankowski, R.; Podlewska, S.
    Conference:
    Paul Ehrlich Euro-PhD Network Virtual Meeting 2021 (rok: 2021, ), Wydawca: Paul Ehrlich Euro-PhD Network
    Data:
    konferencja 2021-07-26-2021-07-28
    Status:
    Published
  4. Interpretability tools in the prediction of properties of biologically active compounds
    Authors:
    Wojtuch, A.; Danel, T.; Jankowski, R.; Podlewska, S.
    Conference:
    4GPCRNet International Symposium (rok: 2022, ), Wydawca: Leipzig University
    Data:
    konferencja 2022-09-26-2022-09-29
    Status:
    Published
  5. Optimization of compounds ADMET properties via machine-learning-based tools
    Authors:
    Podlewska, S.; Kafel, R.
    Conference:
    The 6th International Electronic Conference on Medicinal Chemistry (rok: 2020, ), Wydawca: MDPI
    Data:
    konferencja 2020-11-01-2020-11-30
    Status:
    Published
  6. Virtual screening protocol towards the search of new non-standard 5-HT7R ligands
    Authors:
    Podlewska, S.; Bugno, R.; Satała, G.; Bojarski, A.J.
    Conference:
    Neuronus 2022 Neuroscience Forum (rok: 2022, ), Wydawca: Nencki Institute of Experimental Biology PAS
    Data:
    konferencja 2022-10-15-2022-10-17
    Status:
    Published
  7. Optimization of pharmacokinetic compound profile of serotonin receptor ligands via machine learning
    Authors:
    Podlewska, S.; Kafel, R.
    Conference:
    1st International Electronic Conference on Biomedicine (rok: 2021, ), Wydawca: MDPI
    Data:
    konferencja 2021-06-01-2021-06-26
    Status:
    Published
  8. SHAP-based tools for ADMET compounds profiling on the example of metabolic stability optimization
    Authors:
    Wojtuch, A.; Jankowski, R.; Podlewska, S.
    Conference:
    7th International Electronic Conference on Medicinal Chemistry (rok: 2021, ), Wydawca: MDPI
    Data:
    konferencja 2021-11-01-2021-11-30
    Status:
    Published
  9. Not only affinity - machine-learning-based tools for optimization of ligand physicochemical properties
    Authors:
    Kafel, R.; Podlewska, S.
    Conference:
    EMFC-ISMC&EFMC-YMCS (rok: 2020, ), Wydawca: The European Federation for Medicinal Chemistry
    Data:
    konferencja 44083
    Status:
    Published
  10. Optimization of Metabolic Stability of Ligands of Serotonin Receptor 5-HT7 Using SHAP Values
    Authors:
    Pocha, A.; Jankowski, R.; Podlewska, S.
    Conference:
    1st International Electronic Conference on Biomedicine (rok: 2021, ), Wydawca: MDPI
    Data:
    konferencja 2021-06-01-2021-06-26
    Status:
    Published
  11. Profiling compound ADMET properties with the assistance of SHAP values
    Authors:
    Wojtuch, A.; Jankowski, R.; Podlewska, S.
    Conference:
    The Fifth General Meeting of the European Research Network on Signal Transduction: Bridging Perspectives and Networking in Signal Transduction Research (rok: 2021, ), Wydawca: University of Bari
    Data:
    konferencja 2021-10-04-2021-10-08
    Status:
    Published
  1. Post-processing of Docking Results: Tools and Strategies
    Authors:
    Podlewska, S.; Bojarski, A.J.
    Book:
    Molecular Docking for Computer-Aided Drug Design. Fundamentals, Techniques, Resources and Applications (rok: 2021, tom: 1, strony: 57-74), Wydawca: Academic Press
    Status:
    Published

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