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Virtual High Throughput Screening (vHTS) derivation of a cross-immunity model for the Influenza-A Virus Infections.

2013/09/B/NZ2/00121

Keywords

Descriptors

  • NZ2_1: Genetyka molekularna
  • NZ2_10: Modelowanie i symulacje biologiczne
  • NZ2_11: Epidemiologia genetyczna

Panel

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

Host institution

Uniwersytet Warszawski, Centrum Nowych Technologii Uniwersytetu Warszawskiego

Voivodeship: mazowieckie

Other projects carried out by the institution »

Principal investigator (from the host institution)

dr hab. Dariusz Michał Plewczyński

Number of co-investigators in the project: 5

Call

OPUS 5 – announced on 2013-03-15

Amount awarded
987 900 PLN
Project start date
2014-02-17
Project end date
2017-09-16
Project duration
43 months (the same as in the proposal)
Project status
Project settled

Equipment purchased [PL]

  1. Jednostka obliczeniowa, który będzie używana jako serwer internetowy oraz prototyp rozwiązania w większej skali.. Cost: 20 000 PLN
  2. Komputery mobilne dla wykonawców projektu (3 pcs). Cost: 30 000 PLN
  3. Komputery robocze dla wykonawców projektu (3 pcs). Cost: 45 000 PLN
  4. Oprogramowanie biomolekularne Schrodiner lub podobne, o tej samej, porównywalnej lub lepszej funkcjonalności.. Cost: 29 000 PLN
  5. Oprogramowanie biomolekularne do dokowania: GOLD lub podobne, o tej samej, porównywalnej lub lepszej funkcjonalności.. Cost: 24 000 PLN
  6. komputery robocze dla wykonawców projektu.
  7. oprogramowanie biomolekularne Tripos Sybyl i/lub Accelrys Discovery Studio lub podobne, o tej samej, porównywalnej lub lepszej funkcjonalności.. Cost: 25 000 PLN
  8. oprogramowanie biomolekularne eHiTS lub podobne, o tej samej, porównywalnej lub lepszej funkcjonalności.. Cost: 31 000 PLN

Information in the final report

Publication in academic press/journals (20)

  1. 3D-GNOME: an integrated web service for structural modeling of the 3D genome

    Authors:
    Szalaj P, Michalski PJ, Wróblewski P, Tang Z, Kadlof M, Mazzocco G, Ruan Y, Plewczynski D
    Academic press:
    Nucleic Acids Res (year: 2016, volume: 44, pages: 288-293), Publisher: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/nar/gkw437 – link to the publication

  2. Computational inference of H3K4me3 and H3K27ac domain length

    Authors:
    Zubek J, Stitzel ML, Ucar D, Plewczynski D
    Academic press:
    PeerJ (year: 2016, volume: -, pages: -), Publisher: PeerJ Inc.
    Status:
    Published
    DOI:
    10.7717/peerj.1750 – link to the publication

  3. PDP-CON: prediction of domain/linker residues in protein sequences using a consensus approach.

    Authors:
    Chatterjee P, Basu S, Zubek J, Kundu M, Nasipuri M, Plewczynski D
    Academic press:
    J Mol Model (year: 2016, volume: 22(4), pages: 22-72), Publisher: Springer
    Status:
    Published
    DOI:
    10.1007/s00894-016-2933-0 – link to the publication

  4. 3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale

    Authors:
    Mazzocco G, Lazniewski M, Migdał P, Szczepińska T, Radomski JP, Plewczynski D
    Academic press:
    Database (year: 2016, volume: -, pages: -), Publisher: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/database/baw130 – link to the publication

  5. Novel neuro-audiological findings and further evidence for TWNK involvement in Perrault syndrome

    Authors:
    Ołdak M, Oziębło D, Pollak A, Stępniak I, Lazniewski M, Lechowicz U, Kochanek K, Furmanek M, Tacikowska G, Plewczynski D, Wolak T, Płoski R, Skarżyński H
    Academic press:
    J Trans Med (year: 2017, volume: 15(1), pages: -), Publisher: BioMed Central
    Status:
    Published
    DOI:
    10.1186/s12967-017-1129-4 – link to the publication

  6. Computational Approach to Dendritic Spine Taxonomy and Shape Transition Analysis

    Authors:
    Bokota G, Magnowska M, Kuśmierczyk T, Łukasik M, Roszkowska M, Plewczynski D
    Academic press:
    Front Comput Neurosci (year: 2016, volume: -, pages: -), Publisher: Frontiers Inc.
    Status:
    Published
    DOI:
    10.3389/fncom.2016.00140 – link to the publication

  7. An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

    Authors:
    Szałaj P, Tang Z, Michalski P, Pietal MJ, Luo OJ, Sadowski M, Li X, Radew K, Ruan Y, Plewczynski D
    Academic press:
    Genome Res (year: 2016, volume: 26(12), pages: 1697-1709), Publisher: CSH Press
    Status:
    Published
    DOI:
    10.1101/gr.205062.116 – link to the publication

  8. Multi-level machine learning prediction of protein-protein interactions in Saccharomyces cerevisiae

    Authors:
    Zubek J, Tatjewski M, Boniecki A, Mnich M, Basu S, Plewczynski D.
    Academic press:
    PeerJ (year: 2015, volume: -, pages: -), Publisher: PeerJ Inc.
    Status:
    Published
    DOI:
    10.7717/peerj.1041 – link to the publication

  9. CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

    Authors:
    Tang Z, Luo OJ, Li X, Zheng M, Zhu JJ, Szalaj P, Trzaskoma P, Magalska A, Wlodarczyk J, Ruszczycki B, Michalski P, Piecuch E, Wang P, Wang D, Tian SZ, Penrad-Mobayed M, Sachs LM, Ruan X, Wei CL, Liu ET, Wilczynski GM, Plewczynski D, Li G, Ruan Y.
    Academic press:
    Cell (year: 2015, volume: 163, pages: 1611-1627), Publisher: Elsevier Inc.
    Status:
    Published
    DOI:
    10.1016/j.cell.2015.11.024 – link to the publication

  10. The Proline-Rich Region of Glyceraldehyde-3-Phosphate Dehydrogenase from Human Sperm May Bind SH3 Domains, as Revealed by a Bioinformatic Study of Low-Complexity Protein Segments

    Authors:
    Marcin Tatjewski, Aleksandra Gruca, Dariusz Plewczynski, Marcin Grynberg
    Academic press:
    Molecular Reproduction & Development (year: 2016, volume: 83, pages: 144-148), Publisher: Wiley
    Status:
    Published
    DOI:
    10.1002/mrd.22606 – link to the publication

  11. Detecting reliable non interacting proteins (NIPs) significantly enhancing the computational prediction of protein-protein interactions using machine learning methods

    Authors:
    Srivastava A, Mazzocco G, Kel A, Wyrwicz LS, Plewczynski D
    Academic press:
    Molecular BioSystems (year: 2016, volume: 12, pages: 778-785), Publisher: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/C5MB00672D – link to the publication

  12. A combined systems and structural modeling approach repositions antibiotics for Mycoplasma genitalium

    Authors:
    Kazakiewicz D, Karr JR, Langner KM, Plewczynski D
    Academic press:
    Computational Biology and Chemistry (year: 2015, volume: 59, pages: 91-97), Publisher: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.compbiolchem.2015.07.007 – link to the publication

  13. Binding Activity Prediction of Cyclin-Dependent Inhibitors

    Authors:
    Saha I, Rak B, Bhowmick SS, Maulik U, Bhattacharjee D, Koch U, Lazniewski M, Plewczynski D
    Academic press:
    Journal of Chemical Information and Modeling (year: 2015, volume: 55, pages: 1469-1482), Publisher: ACS Publications
    Status:
    Published
    DOI:
    10.1021/ci500633c – link to the publication

  14. Role of the host genetic variability in the influenza A virus susceptibility

    Authors:
    Ana Carolina Arcanjo, Giovanni Mazzocco, Silviene Fabiana de Oliveira, Dariusz Plewczynski and Jan P. Radomski
    Academic press:
    Acta Biochimica Polonica (year: 2014, volume: 61, pages: 403-419), Publisher: The Journal of the Polish Biochemical Society and of the Committee of Biochemistry and Biophysics Polish Academy of Sciences
    Status:
    Published
    DOI:
    link to the publication

  15. Mapping of the influenza A hemagglutinin serotypes evolution by the ISSCOR method

    Authors:
    Jan Radomski ,Piotr Słonimski ,Włodzimierz Zagórski-Ostoja ,Piotr Borowicz
    Academic press:
    Acta Biochimica Polonica (year: 2014, volume: 61, pages: 441-451), Publisher: The Journal of the Polish Biochemical Society and of the Committee of Biochemistry and Biophysics Polish Academy of Sciences
    Status:
    Published
    DOI:
    link to the publication

  16. Ensemble learning prediction of protein-protein interactions using proteins functional annotations

    Authors:
    Saha I, Zubek J, Klingström T, Forsberg S, Wikander J, Kierczak M, Maulik U, Plewczynski D.
    Academic press:
    Mol Biosyst (year: 2014, volume: 10, pages: 820), Publisher: Royal Society of Chemistry
    Status:
    Published
    DOI:
    10.1039/c3mb70486f – link to the publication

  17. 3gClust: Human Protein Cluster Analysis

    Authors:
    Halder AK, Chatterjee P, Nasipuri M, Plewczynski D, Basu S.
    Academic press:
    IEEE/ACM Trans Comput Biol Bioinform (year: 2018, volume: -, pages: 46023), Publisher: IEEE
    Status:
    Published
    DOI:
    10.1109/TCBB.2018.2840996 – link to the publication

  18. Social adaptation in multi-agent model of linguistic categorization is affected by network information flow

    Authors:
    Julian Zubek, Michał Denkiewicz, Juliusz Barański, Przemysław Wróblewski, Joanna Rączaszek-Leonardi, Dariusz Plewczynski
    Academic press:
    PLoS One (year: 2017, volume: 12(8), pages: e0182490), Publisher: Public Library of Science
    Status:
    Published
    DOI:
    10.1371/journal.pone.0182490 – link to the publication

  19. RNA structure interactions and ribonucleoprotein processes of the influenza A virus

    Authors:
    Dawson W, Lazniewski M, Plewczynski D
    Academic press:
    Brief Funct Genomics (year: 2018, volume: 17(6), pages: 402-414), Publisher: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bfgp/elx028 – link to the publication

  20. The structural variability of the influenza A hemagglutinin receptor binding site

    Authors:
    Michal Lazniewski, Wayne K Dawson, Teresa Szczepińska , Dariusz Plewczynski
    Academic press:
    Briefings in Functional Genomics (year: 2018, volume: 17(6), pages: 415-427), Publisher: Oxford Academic
    Status:
    Published
    DOI:
    10.1093/bfgp/elx042 – link to the publication

Articles in post-conference publications (3)

  1. MaER: A New Multiclass Classifier for BindingActivity Prediction of HLA Class II Proteins

    Authors:
    Mazzocco G, Bhowmick S.S., Saha I., Maulik U., Bhattacharjee D., and Plewczynski D.
    Conference:
    PReMI: 6th International Conference on Pattern Recognition and Machine Intelligence (year: 2015, pages: -), Publisher: Springer in Lecture Notes in Computer Science
    Date:
    conference 30/6-3/7
    Status:
    Published

  2. Evaluating multi-level machine learning prediction of protein-protein interactions

    Authors:
    Julian Zubek, Marcin Tatjewski, Subhadip Basu, Dariusz Plewczynski
    Conference:
    2nd Conference of the Project Information Technologies: research and their interdisciplinary applications (year: 2015, pages: -), Publisher: Instytut Podstaw Informatyki PAN
    Date:
    conference 22-24.10.2015
    Status:
    Published

  3. Distributional Proteomics: Modelling amino acid relationships by measuring their patterns of statistical occurrence across proteins

    Authors:
    Marcin Tatjewski, Dariusz Plewczynski
    Conference:
    2nd Conference of the Project Information Technologies: research and their interdisciplinary applications (year: 2015, pages: -), Publisher: Instytut Podstaw Informatyki PAN
    Date:
    conference 22-24.10.2015
    Status:
    Published

Book publications / chapters in book publications (4)

  1. Predicting Post-Translational Modifications from Local Sequence Fragments Using Machine Learning Algorithms: Overview and Best Practices

    Authors:
    Tatjewski M, Kierczak M, Plewczynski D
    Book:
    Prediction of Protein Secondary Structure (year: 2016, volume: 1484, pages: 275-300), Publisher: Springer Protocols
    Status:
    Published

  2. PDP-RF: Protein Domain Boundary Prediction Using Random Forest Classifier

    Authors:
    Piyali Chatterjee, Subhadip Basu, Julian Zubek, Mahantapas Kundu, Mita Nasipuri, Dariusz Plewczynski
    Book:
    Pattern Recognition and Machine Intelligence in the series of Lecture Notes in Computer Science (year: 2015, volume: 9124, pages: 441-450), Publisher: Springer International Publishing
    Status:
    Published

  3. Analysis of Structural Chromosome Variants by Next Generation Sequencing Methods

    Authors:
    Plewczynski D, Gruca S, Szałaj P, Gulik K, de Oliveira SF and Malhotra A.
    Book:
    Clinical Applications for Next-Generation Sequencing (year: 2015, volume: -, pages: 39-61), Publisher: Elsevier
    Status:
    Published

  4. Analysis of Next-Generation Sequencing Data of miRNA for the Prediction of Breast Cancer

    Authors:
    Indrajit Saha, Shib Sankar Bhowmick, Filippo Geraci, Marco Pellegrini, Debotosh Bhattacharjee, Ujjwal Maulik, Dariusz Plewczynski
    Book:
    SEMCCO 2015: Swarm, Evolutionary, and Memetic Computing in Lecture Notes in Computer Science book series (LNCS) (year: 2015, volume: 9873, pages: 116-127), Publisher: Springer
    Status:
    Published
    DOI:
    link to the publication

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Graphic design and implementation: Jakub Piotrowski