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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Structural RNomics

2012/04/A/NZ2/00455

Keywords:

RNA sequence analysis structure prediction experimental structure determination molecular evolution

Descriptors:

  • NZ2_7: Bioinformatics
  • NZ1_4: Structural biology
  • NZ1_2: Biochemistry

Panel:

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

Host institution :

Międzynarodowy Instytut Biologii Molekularnej i Komórkowej

woj. mazowieckie

Other projects carried out by the institution 

Principal investigator (from the host institution):

prof. Janusz Bujnicki 

Number of co-investigators in the project: 13

Call: MAESTRO 2 - announced on 2011-12-15

Amount awarded: 3 000 000 PLN

Project start date (Y-m-d): 2012-10-08

Project end date (Y-m-d): 2018-04-07

Project duration:: 66 months (the same as in the proposal)

Project status: Project settled

Equipment purchased [PL]

  1. Dedykowany serwer obliczeniowy wraz z systemem wspierającym bazę danych - uzupełnienie.
  2. Dedykowany serwer obliczeniowy wraz z systemem wspierającym bazę danych (200 000 PLN)
  3. Zbiornik Dewara do przewożenia kryształów w ciekłym azocie.
  4. Inkubator do automatycznego systemu monitorowania prób krystalizacji (300 000 PLN)
  5. Rozbudowa rozproszonego systemu dyskowego ISILON (152 151 PLN)

Information in the final report

  • Publication in academic press/journals (14)
  • Book publications / chapters in book publications (1)
  1. Coarse-grained modeling of RNA 3D structure
    Authors:
    Wayne K. Dawson, Maciej Maciejczyk, Elzbieta J. Jankowska, Michal J. Boniecki, Janusz M. Bujnicki
    Academic press:
    Methods (rok: 2016, tom: 103, strony: 138-156), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.ymeth.2016.04.026 - link to the publication
  2. Computational modeling of RNA 3D structures and interactions
    Authors:
    Dawson WK, Bujnicki JM
    Academic press:
    Current Opinion in Structural Biology (rok: 2016, tom: 37, strony: 22-28), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.sbi.2015.11.007 - link to the publication
  3. MODOMICS: a database of RNA modification pathways. 2017 update
    Authors:
    Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki T, de Crécy-Lagard V, Ross R, Limbach P, Kotter A, Helm M, Bujnicki JM
    Academic press:
    Nucleic Acids Research (rok: 2018, tom: 46, strony: D303–D307), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkx1030 - link to the publication
  4. Specific interaction of zinc finger protein Com with RNA and the crystal structure of a self-complementary RNA duplex recognized by Com.
    Authors:
    Nowacka M, Fernandes H, Kiliszek A, Bernat A, Lach G, Bujnicki JM
    Academic press:
    PLoS ONE (rok: 2019, tom: 14(4), strony: e0214481), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0214481 - link to the publication
  5. Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods
    Authors:
    Patel T, Chojnowski G, Astha, Koul A, McKenna S, Bujnicki JM
    Academic press:
    Methods (rok: 2016, tom: Volumes 118–119, strony: 146-162), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.ymeth.2016.12.002 - link to the publication
  6. Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2' 5'-Oligoadenylate Synthetase family.
    Authors:
    Deo S, Patel TR, Chojnowski G, Koul A, Dzananovic E, McEleney K, Bujnicki JM, McKenna SA
    Academic press:
    RNA (rok: 2015, tom: Volume 190, strony: 236-249), Wydawca: RNA Society/Cold Spring Harbor
    Status:
    Published
    DOI:
    10.1016/j.jsb.2015.04.005 - link to the publication
  7. Impact of the structural integrity of the three-way junction of adenovirus VAI RNA on PKR inhibition
    Authors:
    Dzananovic E, Astha, Chojnowski G, Deo S, Booy EP, Padilla-Meier P, McEleney K, Bujnicki JM, Patel TR, McKenna SA
    Academic press:
    PLoS One (rok: 2017, tom: online, strony: published online), Wydawca: PLOS
    Status:
    Published
    DOI:
    10.1371/journal.pone.0186849 - link to the publication
  8. Matching tRNA modifications in humans to their known and predicted enzymes
    Authors:
    de Crécy-Lagard V, Boccaletto P, Mangleburg CG, Sharma P, Lowe TM, Leidel SA, Bujnicki JM
    Academic press:
    Nucleic Acids Research (rok: 2019, tom: 47(5), strony: 2143-2159), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkz011 - link to the publication
  9. RNArchitecture: a database and a classification system of RNA families, with a focus on structural information
    Authors:
    Boccaletto P, Magnus M, Almeida C, Zyla A, Astha, Pluta R, Baginski B, Jankowska E, Dunin-Horkawicz S, Wirecki T, Boniecki M, Stefaniak F, Bujnicki JM
    Academic press:
    Nucleic Acids Research (rok: 2018, tom: 46, strony: D202-D205), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkx966 - link to the publication
  10. Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs
    Authors:
    Chawla M, Chermak E, Zhang Q, Bujnicki JM, Oliva R, Cavallo L
    Academic press:
    Nucleic Acids Research (rok: 2017, tom: 45, strony: 11019-11032), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkx757 - link to the publication
  11. RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures
    Authors:
    Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E
    Academic press:
    RNA (rok: 2015, tom: Vol 21, strony: 1066-84), Wydawca: RNA Society/Cold Spring Harbour
    Status:
    Published
    DOI:
    10.1261/rna.049502.114. - link to the publication
  12. RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme
    Authors:
    Petrov AI, Kay SJE, Kalvari I, Howe KL, Gray KA, Bruford EA, Kersey PJ, Cochrane G, Finn RD, Bateman A, Kozomara A, Griffiths-Jones S, Frankish A, Zwieb CW, Lau BY, Williams KP, Chan PP, Lowe TM, Cannone JJ, Gutell RR, Machnicka MA, Bujnicki JM, Yoshihama M, Kenmochi N, Chai B, Cole JR, Szymanski M, Karlowski WM, Wood V, Huala E, Berardini TZ, Zhao Y, Chen R, Zhu W, Paraskevopoulou MD, Vlachos IS, Hatzigeorgiou AG, SILVA team , Ma L, Zhang Z, Puetz J, Stadler PF, McDonald D, Basu S, Fey P, Engel SR, Cherry JM, Volders P, Mestdagh P, Wower J, Clark M, Quek XC, Dinger ME
    Academic press:
    RNA (rok: 2017, tom: 23, strony: 655–672), Wydawca: Cold Spring Harbor
    Status:
    Published
    DOI:
    10.1261/rna.060368.116 - link to the publication
  13. SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments
    Authors:
    Piatkowski P, Jablonska J, Zyla A, Niedzialek D, Matelska D, Jankowska E, Walen T, Dawson WK, Bujnicki JM
    Academic press:
    Nucleic Acids Research (rok: 2017, tom: 45, strony: 150), Wydawca: Oxford University Press
    Status:
    Published
    DOI:
    10.1093/nar/gkx631 - link to the publication
  14. tRNAmodpred: a computational method for predicting posttranscriptional modifications in tRNAs Methods
    Authors:
    Magdalena A. Machnicka, Stanislaw Dunin-Horkawicz, Valerie de Crécy-Lagard, Janusz M. Bujnicki
    Academic press:
    Methods (rok: 2016, tom: 107, strony: 34-41), Wydawca: Elsevier
    Status:
    Published
    DOI:
    10.1016/j.ymeth.2016.03.013 - link to the publication
  1. RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS
    Authors:
    Pawel Piatkowski, Joanna M. Kasprzak, Deepak Kumar, Marcin Magnus, Grzegorz Chojnowski, Janusz M. Bujnicki
    Book:
    RNA Structure Determination (rok: 2016, tom: 1490, strony: 217-235), Wydawca: Springer
    Status:
    Published

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