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 " Computational Chemical Linguistics" and its Applications to the Efficient Planning of Multisep Chemical Syntheses.

2014/12/W/ST5/00592

Keywords:

Linguistics chemical synthesis planning

Descriptors:

  • ST5_23:
  • ST1_15: Mathematical aspects of computer science

Panel:

ST5 - Materials: materials synthesis, structure-properties relations, advanced and functional materials with designed properties, (macro)molecular architecture, material engineering

Host institution :

Instytut Chemii Organicznej PAN

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Bartosz Grzybowski 

Number of co-investigators in the project: 19

Call: SYMFONIA 2

Amount awarded: 6 298 680 PLN

Project start date (Y-m-d): 2014-12-11

Project end date (Y-m-d): 2020-12-10

Project duration:: 72 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Elementy do konstrukcji automatycznej linii do zaawansowanej syntezy organicznej (450 000 PLN)
  2. Komputer stacjonarny (6 000 PLN)
  3. Notebook (7 szt.) (28 000 PLN)
  4. Serwer plików z dyskami pamięci (11 587 PLN)
  5. Notebook (2 szt.) (10 000 PLN)
  6. Notebook z oprogramowaniem (3 szt.) (21 000 PLN)
  7. Rzutnik multimedialny (4 000 PLN)
  8. Wysokowydajny serwer (54 500 PLN)
  9. Drukarka sieciowa laserowa (2 000 PLN)
  10. Komputer stacjonarny (8 000 PLN)
  11. Oprogramowanie LabVIEW.
  12. Wyparka próżniowa (25 000 PLN)
  13. Wysokowydajny serwer (70 000 PLN)

Information in the final report

  • Publication in academic press/journals (22)
  • Articles in post-conference publications (2)
  1. A Priori Estimation of Organic Reaction Yields
    Authors:
    Dr. Fateme S. Emami, Dr. Amir Vahid, Elizabeth K. Wylie, Sara Szymkuć, Dr. Piotr Dittwald, Karol Molga and Prof. Bartosz A. Grzybowski
    Academic press:
    Angewandte Chemie International Edition (rok: 2015, tom: vol 54 Issue 37, strony: 10797–10801), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/anie.201503890 - link to the publication
  2. Concentric liquid reactors for chemical synthesis and separation
    Authors:
    O. Cybulski, M. Dygas, B. Mikulak-Klucznik, M. Siek, T. Klucznik, S. Yeol Choi, R. J. Mitchell, Y. I. Sobolev, B. A. Grzybowski
    Academic press:
    Nature (rok: 2020, tom: 586, strony: 57-63), Wydawca: Springer Nature Limited
    Status:
    Published
    DOI:
    10.1038/s41586-020-2768-9 - link to the publication
  3. Stylometry with R: a package for computational text analysis.
    Authors:
    Eder, M., Kestemont, M. and Rybicki, J.
    Academic press:
    R Journal (rok: 2015, tom: 8(1), strony: 45306), Wydawca: R project
    Status:
    Published
    DOI:
    brak - link to the publication
  4. masstodon: A Tool for Assigning Peaks and Modeling Electron Transfer Reactions in Top-Down Mass Spectrometry
    Authors:
    Łącki MK, Lermyte F, Miasojedow B, Startek MP, Sobott F, Valkenborg D, Gambin A.
    Academic press:
    Analytical chemistry (rok: 2019, tom: 91(3), strony: 1801-1807), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1021/acs.analchem.8b01479 - link to the publication
  5. Inferring Molecular Processes Heterogeneity from Transcriptional Data
    Authors:
    Krzysztof Gogolewski, Weronika Wronowska, Agnieszka Lech, Bogdan Lesyng, and Anna Gambin
    Academic press:
    BioMed Research International (rok: 2017, tom: 2017, strony: 45305), Wydawca: Hindawi Publishing Corporation
    Status:
    Published
    DOI:
    10.1155/2017/6961786 - link to the publication
  6. Linguistic measures of chemical diversity and the keywords" of molecular collections
    Authors:
    M. Woźniak, A. Wołos, U. Modrzyk, R. L. Górski, J. Winkowski, M. Bajczyk, S. Szymkuć, B. A. Grzybowski, M. Eder
    Academic press:
    Scientific Reports (rok: 2018, tom: 8, strony: 7598), Wydawca: Nature
    Status:
    Published
    DOI:
    10.1038/s41598-018-25440-6 - link to the publication
  7. Predicting the outcomes of organic reactions via machine learning: are current descriptors sufficient?
    Authors:
    G. Skoraczyński, P. Dittwald, B. Miasojedow, S. Szymkuć, E. P. Gajewska, B. A. Grzybowski & A. Gambin
    Academic press:
    Scientific Reports (rok: 2017, tom: 7, strony: 45300), Wydawca: Nature
    Status:
    Published
    DOI:
    10.1038/s41598-017-02303-0 - link to the publication
  8. Conformational Space and Stability of ETD Charge Reduction Products of Ubiquitin
    Authors:
    Frederik Lermyte, Mateusz Krzysztof Łącki, Dirk Valkenborg, Anna Gambin, Frank Sobott
    Academic press:
    J. Am. Soc. Mass Spectrom. (rok: 2017, tom: 28(1), strony: 69-76), Wydawca: ACS Publications
    Status:
    Published
    DOI:
    10.1007/s13361-016-1444-7 - link to the publication
  9. IsoSpec: Hyperfast Fine Structure Calculator
    Authors:
    Mateusz K. Łącki, Michał Startrek, Dirk Valkenborg, and Anna Gambin
    Academic press:
    Analytical Chemistry (rok: 2017, tom: 89(6), strony: 3272-3277), Wydawca: ACS
    Status:
    Published
    DOI:
    10.1021/acs.analchem.6b01459 - link to the publication
  10. Minimal-uncertainty prediction of general drug-likeness based on Bayesian neural networks
    Authors:
    W. Beker, A. Wołos, S. Szymkuć, B. A. Grzybowski
    Academic press:
    Nature Machine Intelligence (rok: 2020, tom: 2, strony: 457-465), Wydawca: Springer Nature Limited
    Status:
    Published
    DOI:
    10.1038/s42256-020-0209-y - link to the publication
  11. Selection of cost-effective yet chemically diverse pathways from the networks of computer-generated retrosynthetic plans
    Authors:
    Badowski T., Molga K., Grzybowski B.A.
    Academic press:
    Chemical Science (rok: 2019, tom: 10, strony: 4640-4651), Wydawca: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/C8SC05611K - link to the publication
  12. Synthetic connectivity, emergence, and self-regeneration in the network of prebiotic chemistry.
    Authors:
    1.Wołos A., Roszak R., Żądło-Dobrowolska A., Beker W., Mikulak-Klucznik B., Spólnik G., Dygas M., Szymkuć S., Grzybowski B.A.
    Academic press:
    Science (rok: 2020, tom: 369, strony: eaaw1955), Wydawca: American Association for the Advancement of Science.
    Status:
    Published
    DOI:
    10.1126/science.aaw1955 - link to the publication
  13. Discovery and Enumeration of Organic‐Chemical and Biomimetic Reaction Cycles within the Network of Chemistry
    Authors:
    M. D. Bajczyk, Dr P. Dittwald, A. Wołos, S. Szymkuć, Prof. B. A. Grzybowski
    Academic press:
    Angewandte Chemie - Internatonal Edition (rok: 2018, tom: 57, strony: 2367-2371), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/anie.201712052 - link to the publication
  14. Efficient syntheses of diverse, medicinally relevant targets planned by computer and executed in the laboratory.
    Authors:
    Klucznik T., Mikulak-Klucznik B., McCormack M. P. , Lima H., Szymkuć S., Bhowmick M., Molga K., Zhou Y., Rickershauser L., Gajewska E. P., Toutchkine A., Dittwald P., Startek M. P., Kirkovits G. J., Roszak R., Adamski A., Sieredzińska B., Mrksich M., Trice S. L. J., Grzybowski B. A.
    Academic press:
    Chem (rok: 2018, tom: 4, strony: 522-532), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.chempr.2018.02.002 - link to the publication
  15. Propagation of Oscillating Chemical Signals through Reaction Networks
    Authors:
    Roszak R., Bajczyk M.D., Gajewska E.P., Hołyst R., Grzybowski B.A.
    Academic press:
    Angewandte Chemie International Edition (rok: 2019, tom: 58(14), strony: 4520-4545), Wydawca: Wiley Online Library
    Status:
    Published
    DOI:
    10.1002/anie.201808821 - link to the publication
  16. Automatic mapping of atoms across both simple and complex chemical reactions
    Authors:
    Jaworski W., Szymkuć S., Mikulak-Klucznik B., Piecuch K., Klucznik T., Kaźmierowski M., Rydzewski J., Gambin A., Grzybowski B.A.
    Academic press:
    Nature communications (rok: 2019, tom: 10, strony: 1434), Wydawca: Nature Research
    Status:
    Published
    DOI:
    10.1038/s41467-019-09440-2 - link to the publication
  17. Computational planning of the synthesis of complex natural products
    Authors:
    B. Mikulak-Klucznik, P. Gołębiowska, A. A. Bayly, O. Popik, T. Klucznik, S. Szymkuć, E. P. Gajewska, P. Dittwald, O. Staszewska-Krajewska, W. Beker, T. Badowski, K. A. Scheidt, K. Molga, J. Młynarski, M. Mrksich, B. A. Grzybowski
    Academic press:
    Nature (rok: 2020, tom: 588, strony: 83-88), Wydawca: Springer Nature Limited
    Status:
    Published
    DOI:
    10.1038/s41586-020-2855-y - link to the publication
  18. Computer-Assisted Synthetic Planning: The End of the Beginning
    Authors:
    Sara Szymkuć, Ewa P. Gajewska, Tomasz Klucznik, Karol Molga, Dr. Piotr Dittwald, Dr. Michał Startek, Michał Bajczyk, Prof. Dr. Bartosz A. Grzybowski
    Academic press:
    Angewandte Chemie International Edition (rok: 2016, tom: vol 55 Issue 20, strony: 5904–5937), Wydawca: Wiley
    Status:
    Published
    DOI:
    10.1002/anie.201506101 - link to the publication
  19. Estimation of Rates of Reactions Triggered by Electron Transfer in Top-Down Mass Spectrometry
    Authors:
    Ciach Michał Aleksander, Łącki Mateusz Krzysztof, Miasojedow Błażej, Lermyte Frederik, Valkenborg Dirk, Sobott Frank, and Anna Gambin
    Academic press:
    Journal of Computational Biology (rok: 2017, tom: 24, strony: 45311), Wydawca: Mary Ann Liebert, Inc.
    Status:
    Published
    DOI:
    10.1089/cmb.2017.0156 - link to the publication
  20. Improvement of the k-NN Entropy Estimator with Applications in Systems Biology
    Authors:
    Agata Charzyńska, Anna Gambin
    Academic press:
    Entropy (rok: 2015, tom: 18 (13), strony: 45310), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/e18010013 - link to the publication
  21. Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data
    Authors:
    Neo Christopher Chung, Błażej Miasojedow, Michał Startek, Anna Gambin
    Academic press:
    BMC Bioinformatics (rok: 2019, tom: 20, strony: 644), Wydawca: Springer Nature
    Status:
    Published
    DOI:
    10.1186/s12859-019-3118-5 - link to the publication
  22. Low Entropy Sub-Networks Prevent the Integration of Metabolomic and Transcriptomic Data
    Authors:
    K. Gogolewski, M. Kostecki, A. Gambin
    Academic press:
    Entropy (rok: 2020, tom: 22, strony: 1238), Wydawca: MDPI
    Status:
    Published
    DOI:
    10.3390/e22111238 - link to the publication
  1. Pattern Recognition of Chemical Fingerprints from Large-Scale Databases of Molecules and Reactions
    Authors:
    Neo Christopher Chung, Błażej Miasojedow, Anna Gambin
    Conference:
    12th International Symposium on Bioinformatics Research and Applications (ISBRA) (rok: 2016, ), Wydawca: Springer
    Data:
    konferencja June 5-8
    Status:
    Published
    DOI:
    link to the publication
  2. The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution
    Authors:
    Szymon Majewski, Michał Ciach, Michał Startek, Wanda Niemyska, Błażej Miasojedow i Anna Gambin
    Conference:
    18th International Workshop on Algorithms in Bioinformatics (WABI 2018) (rok: 2018, ), Wydawca: Saarbrücken/Wadern Schloss Dagstuhl - Leibniz-Zentrum für Informatik GmbH, Dagstuhl Publishing August, 2018
    Data:
    konferencja Sierpień 20–22, 2018
    Status:
    Published
    DOI:
    link to the publication

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