Wirecki TK - Search Results

1

MODOMICS: a database of RNA modification pathways. 2017 update.

Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki TK, de Crécy-Lagard V, Ross R, Limbach PA, Kotter A, Helm M, Bujnicki JM. Boccaletto P, et al. Among authors: wirecki tk. Nucleic Acids Res. 2018 Jan 4;46(D1):D303-D307. doi: 10.1093/nar/gkx1030. Nucleic Acids Res. 2018. PMID: 29106616 Free PMC article.

2

RNArchitecture: a database and a classification system of RNA families, with a focus on structural information.

Boccaletto P, Magnus M, Almeida C, Zyla A, Astha A, Pluta R, Baginski B, Jankowska E, Dunin-Horkawicz S, Wirecki TK, Boniecki MJ, Stefaniak F, Bujnicki JM. Boccaletto P, et al. Among authors: wirecki tk. Nucleic Acids Res. 2018 Jan 4;46(D1):D202-D205. doi: 10.1093/nar/gkx966. Nucleic Acids Res. 2018. PMID: 29069520 Free PMC article.

3

RNAProbe: a web server for normalization and analysis of RNA structure probing data.

Wirecki TK, Merdas K, Bernat A, Boniecki MJ, Bujnicki JM, Stefaniak F. Wirecki TK, et al. Nucleic Acids Res. 2020 Jul 2;48(W1):W292-W299. doi: 10.1093/nar/gkaa396. Nucleic Acids Res. 2020. PMID: 32504492 Free PMC article.

4

Modeling of Three-Dimensional RNA Structures Using SimRNA.

Wirecki TK, Nithin C, Mukherjee S, Bujnicki JM, Boniecki MJ. Wirecki TK, et al. Methods Mol Biol. 2020;2165:103-125. doi: 10.1007/978-1-0716-0708-4_6. Methods Mol Biol. 2020. PMID: 32621221

5

Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements.

Manfredonia I, Nithin C, Ponce-Salvatierra A, Ghosh P, Wirecki TK, Marinus T, Ogando NS, Snijder EJ, van Hemert MJ, Bujnicki JM, Incarnato D. Manfredonia I, et al. Among authors: wirecki tk. Nucleic Acids Res. 2020 Dec 16;48(22):12436-12452. doi: 10.1093/nar/gkaa1053. Nucleic Acids Res. 2020. PMID: 33166999 Free PMC article.

6

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.

Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z, Szachniuk M, Rybarczyk A. Gumna J, et al. Int J Mol Sci. 2022 Aug 25;23(17):9630. doi: 10.3390/ijms23179630. Int J Mol Sci. 2022. PMID: 36077037 Free PMC article.

7

RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints.

Baulin EF, Mukherjee S, Moafinejad SN, Wirecki TK, Badepally NG, Jaryani F, Stefaniak F, Amiri Farsani M, Ray A, Rocha de Moura T, Bujnicki JM. Baulin EF, et al. Among authors: wirecki tk. Proteins. 2023 Dec;91(12):1800-1810. doi: 10.1002/prot.26575. Epub 2023 Aug 25. Proteins. 2023. PMID: 37622458

8

A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.

Liwo A, Baranowski M, Czaplewski C, Gołaś E, He Y, Jagieła D, Krupa P, Maciejczyk M, Makowski M, Mozolewska MA, Niadzvedtski A, Ołdziej S, Scheraga HA, Sieradzan AK, Slusarz R, Wirecki T, Yin Y, Zaborowski B. Liwo A, et al. J Mol Model. 2014 Aug;20(8):2306. doi: 10.1007/s00894-014-2306-5. Epub 2014 Jul 15. J Mol Model. 2014. PMID: 25024008 Free PMC article.

9

Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.

Sieradzan AK, Czaplewski C, Krupa P, Mozolewska MA, Karczyńska AS, Lipska AG, Lubecka EA, Gołaś E, Wirecki T, Makowski M, Ołdziej S, Liwo A. Sieradzan AK, et al. Methods Mol Biol. 2022;2376:399-416. doi: 10.1007/978-1-0716-1716-8_23. Methods Mol Biol. 2022. PMID: 34845623

10

A Maximum-Likelihood Approach to Force-Field Calibration.

Zaborowski B, Jagieła D, Czaplewski C, Hałabis A, Lewandowska A, Żmudzińska W, Ołdziej S, Karczyńska A, Omieczynski C, Wirecki T, Liwo A. Zaborowski B, et al. J Chem Inf Model. 2015 Sep 28;55(9):2050-70. doi: 10.1021/acs.jcim.5b00395. Epub 2015 Aug 20. J Chem Inf Model. 2015. PMID: 26263302

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