Publications

0000-0001-5758-9416
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Scopus ID: 14623077600 PBN - polon
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2024 RNA-Puzzles Round V: blind predictions of 23 RNA structures

Topics:

Bu, F., Adam, Y., Adamiak, R.W. [...] Filip Stefaniak [...] et al.
RNA-Puzzles Round V: blind predictions of 23 RNA structures.
Nat Methods, 2024 | DOI: 10.1038/s41592-024-02543-9

IF: 36.1; 5-Year IF: 45.6

2024 SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories

S Naeim Moafinejad, Belisa R H de Aquino, Michał J Boniecki, Iswarya P N Pandaranadar Jeyeram, Grigory Nikolaev, Marcin Magnus, Masoud Amiri Farsani, Nagendar Goud Badepally, Tomasz K Wirecki, Filip Stefaniak, Janusz M Bujnicki
SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories
Nucleic Acids Research, 2024, gkae356; | DOI: 10.1093/nar/gkae356

IF: 14.9 (2022); 5-Year IF: 17.210

2024 MODOMICS: a database of RNA modifications and related information. 2023 update

Topics:

Andrea Cappannini, Angana Ray, Elżbieta Purta, Sunandan Mukherjee, Pietro Boccaletto, S. Naeim Moafinejad, Antony Lechner, Charles Barchet, Bruno Klaholz, Filip Stefaniak, Janusz M. Bujnicki
MODOMICS: a database of RNA modifications and related information. 2023 update
Nucleic Acids Research, Volume 52, Issue D1, 2024, Pages D239–D244 | DOI: 10.1093/nar/gkad1083

IF: 14.9 (2022); 5-Year IF: 17.210

The database described in the paper: https://iimcb.genesilico.pl/modomics/

2024 DEGRONOPEDIA: a web server for proteome-wide inspection of degrons

Topics:

Natalia A Szulc, Filip Stefaniak, Małgorzata Piechota, Anna Soszyńska, Gabriela Piórkowska, Andrea Cappannini, Janusz M Bujnicki, Chiara Maniaci, Wojciech Pokrzywa
DEGRONOPEDIA: a web server for proteome-wide inspection of degrons
Nucleic Acids Research, 2024; gkae238 | DOI: 10.1093/nar/gkae238

IF: 14.9 (2022); 5-Year IF: 17.210

The webserver described in the paper: https://degronopedia.com/

2023 RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints

Topics:

Eugene F. Baulin; Sunandan Mukherjee; S. Naeim Moafinejad; Tomasz K. Wirecki; Nagendar Goud Badepally; Farhang Jaryani; Filip Stefaniak; Masoud Amiri Farsani; Angana Ray; Tales Rocha de Moura; Janusz M. Bujnicki
RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints.
Proteins: Structure, Function, and Bioinformatics 2023 | DOI: 10.1002/prot.26575

IF: 2.9

2023 Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA

Topics:

Natalia A Szulc, Zuzanna Mackiewicz, Janusz M Bujnicki, Filip Stefaniak
Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA
Briefings in Bioinformatics, bbad187 2023 | DOI: 10.1093/bib/bbad187

IF: 13.994

2022 fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions

Topics:

Natalia A Szulc, Zuzanna Mackiewicz, Janusz M Bujnicki, Filip Stefaniak
fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions
PLOS Computational Biology 18(6): e1009783 2022 | DOI: 10.1371/journal.pcbi.1009783

IF: 4.779 (^{PLOS does not consider Impact Factor to be a reliable or useful metric to assess the performance of individual articles.})

2022 Design, Synthesis, and Development of pyrazolo[1,5-a]pyrimidine Derivatives as a Novel Series of Selective PI3Kδ Inhibitors: Part I—Indole Derivatives

Topics:

Stypik, Mariola, Marcin Zagozda, Stanisław Michałek, Barbara Dymek, Daria Zdżalik-Bielecka, Maciej Dziachan, Nina Orłowska, Paweł Gunerka, Paweł Turowski, Joanna Hucz-Kalitowska, Aleksandra Stańczak, Paulina Stańczak, Krzysztof Mulewski, Damian Smuga, Filip Stefaniak, Lidia Gurba-Bryśkiewicz, Arkadiusz Leniak, Zbigniew Ochal, Mateusz Mach, Karolina Dzwonek, Monika Lamparska-Przybysz, Krzysztof Dubiel, and Maciej Wieczorek.
Design, Synthesis, and Development of pyrazolo[1,5-a]pyrimidine Derivatives as a Novel Series of Selective PI3Kδ Inhibitors: Part I—Indole Derivatives
Pharmaceuticals 15, no. 8: 949, 2022 | DOI: 10.3390/ph15080949

IF: 5.215; 5-Year IF: 5.711

2022 MODOMICS: a database of RNA modification pathways. 2021 update

Topics:

Pietro Boccaletto, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Elżbieta Purta, Małgorzata Kurkowska, Niloofar Shirvanizadeh, Eliana Destefanis, Paula Groza, Gülben Avşar, Antonia Romitelli, Pınar Pir, Erik Dassi, Silvestro G Conticello, Francesca Aguilo, Janusz M Bujnicki
MODOMICS: a database of RNA modification pathways. 2021 update
Nucleic Acids Research, Volume 50, Issue D1, Pages D231–D235, 7 January 2022 | DOI: 10.1093/nar/gkab1083

IF: 19.160; 5-Year IF: 17.210

The database described in the paper: https://iimcb.genesilico.pl/modomics/

2021 (book chapter) Computational Modeling Methods for 3D Structure Prediction of Ribozymes

Topics:

Pritha Ghosh, Chandran Nithin, Astha Joshi, Filip Stefaniak, Tomasz K. Wirecki, Janusz M. Bujnicki
Computational Modeling Methods for 3D Structure Prediction of Ribozymes
Ribozymes, Volume 2, Chapter 33; pp 861-881, 2021 | DOI: 10.1002/9783527814527.ch33

2021 AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses

Topics:

Filip Stefaniak, Janusz M Bujnicki
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
PLOS Computational Biology, February 1, 2021 | DOI: journal.pcbi.1008309

IF: 4.700

AnnapuRNA repository: github

2020 Luciferase reporter assay for small-molecule inhibitors of MIR92b-3p function: Screening cyanopeptolins produced by Nostoc from the Baltic Sea

Topics:

Paweł Brzuzan, Hanna Mazur-Marzec, Maciej Florczyk, Filip Stefaniak, Anna Fidor, Robert Konkel, Maciej Woźny
Luciferase reporter assay for small-molecule inhibitors of MIR92b-3p function: Screening cyanopeptolins produced by Nostoc from the Baltic Sea
Toxicology in Vitro, 2020, Volume 68, 104951 | DOI: 10.1016/j.tiv.2020.104951

IF: 2.959

2020 RNAProbe: a web server for normalization and analysis of RNA structure probing data

Topics:

Tomasz K Wirecki, Katarzyna Merdas, Agata Bernat, Michał J Boniecki, Janusz M Bujnicki, and Filip Stefaniak
RNAProbe: a web server for normalization and analysis of RNA structure probing data
Nucleic Acids Research, 2020, Volume 48, Issue W1, Pages W292–W299 | DOI: 10.1093/nar/gkaa396

IF: 16.971; 5-Year IF: 15.542

The web server described in the paper: https://rnaprobe.genesilico.pl/

2020 Benzoxazepine-Derived Selective, Orally Bioavailable Inhibitor of Human Acidic Mammalian Chitinase

Topics:

Gleb Andryianau, Michal Kowalski, Michal C. Piotrowicz, Adam A. Rajkiewicz, Barbara Dymek, Piotr L. Sklepkiewicz, Elzbieta Pluta, Filip Stefaniak, Wojciech Czestkowski, Sylwia Olejniczak, Marzena Mazur, Piotr Niedziejko, Robert Koralewski, Krzysztof Matyszewski, Mariusz Gruza, Agnieszka Zagozdzon, Magdalena Salamon, Aleksandra Rymaszewska, Mikolaj Welzer, Karolina Dzwonek, Jakub Golab, Jacek Olczak, Agnieszka Bartoszewicz, and Adam Golebiowski

ACS Med. Chem. Lett. 2020, 11, 6, Pages 1228–1235 | DOI: 10.1021/acsmedchemlett.0c00092

IF: 3.975 (2019)

2019 Development of Dual Chitinase Inhibitors as Potential New Treatment for Respiratory System Diseases

Topics:

Marzena Mazur, Barbara Dymek, Robert Koralewski, Piotr Sklepkiewicz, Sylwia Olejniczak, Marcin Mazurkiewicz, Michał Piotrowicz, Magdalena Salamon, Karol Jędrzejczak, Agnieszka Zagozdzon, Wojciech Czestkowski, Krzysztof Matyszewski, Bartłomiej Borek, Agnieszka Bartoszewicz, Elżbieta Pluta, Aleksandra Rymaszewska, Witold Mozga, Filip Stefaniak, Paweł Dobrzański, Karolina Dzwonek, Jakub Golab, Adam Golebiowski, and Jacek Olczak
Development of Dual Chitinase Inhibitors as Potential New Treatment for Respiratory System Diseases
Journal of Medicinal Chemistry, 62 (15), 2019, Pages 7126-7145 | DOI: 10.1021/acs.jmedchem.9b00681

IF: 6.205 (2019)

2019 Structural bases of peptidoglycan recognition by lysostaphin SH3b domain

Topics:

Paweł Mitkowski, Elżbieta Jagielska, Elżbieta Nowak, Janusz M. Bujnicki, Filip Stefaniak, Dorota Niedziałek, Matthias Bochtler & Izabela Sabała
Structural bases of peptidoglycan recognition by lysostaphin SH3b domain
Scientific Reports, volume 9, 5965, 2019 | DOI: 10.1038/s41598-019-42435-z

IF: 4.122; 5-Year IF: 4.609

2018 Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5′ termini

Topics:

Diana Toczydlowska-Socha, Magdalena M. Zielinska, Malgorzata Kurkowska, Astha, Catarina F. Almeida, Filip Stefaniak, Elzbieta Purta, Janusz M. Bujnicki
Phil. Trans. R. Soc. B 2018 373, 20180161, 2018 | DOI: 10.1098/rstb.2018.0161

IF: 5.666 (2017); 5-Year IF: 7.192

Visible also as: D Toczydlowska-Socha, M Kurkowska, M Zielinska, A Joshi, C Almeida, E Purta, F Stefaniak, J Bujnicki, FEBS OPEN BIO 9, 121-122, 2019.

2019 (conference paper) Riboswitch-ligand structure determination using an integrative structural biology approach

Topics:

A Ponce-Salvatierra, R Pluta, E Skowronek, M Orlowska, B Baginski, M Kurkowska, E Purta, P Ghosh, T Wirecki, F Stefaniak, JM Bujnicki
FEBS OPEN BIO, 9, 243-243, 2019.

2018 Synthesis and characterization of novel classes of PDE10A inhibitors - 1H-1,3-benzodiazoles and imidazo[1,2-a]pyrimidines

Topics:

Rafał Moszczyński-Pętkowski, Jakub Majer, Małgorzata Borkowska, Łukasz Bojarski, Sylwia Janowska, Mikołaj Matłoka, Filip Stefaniak, Damian Smuga, Katarzyna Bazydło, Krzysztof Dubiel, Maciej Wieczorek
European Journal of Medicinal Chemistry 155, 15 July, 2018, Pages 96-116 | DOI: 10.1016/j.ejmech.2018.05.043

IF: 4.519; 5-Year IF: 4.187

2018 Discovery of selective, orally bioavailable inhibitor of mouse chitotriosidase.

Topics:

Mazur M, Bartoszewicz A, Dymek B, Salamon M, Andryianau G, Kowalski M, Olejniczak S, Matyszewski K, Pluta E, Borek B, Stefaniak F, Zagozdzon A, Mazurkiewicz M, Koralewski R, Czestkowski W, Piotrowicz M, Niedziejko P, Gruza MM, Dzwonek K, Golebiowski A, Golab J, Olczak J
Bioorg Med Chem Lett. Volume 28, Issue 3, 1 February 2018, Pages 310-314 | DOI: 10.1016/j.bmcl.2017.12.047

IF: 2.454; 5-Year IF: 2.286

2018 Novel inhibitors of the rRNA ErmC′ methyltransferase to block resistance to Macrolides, Lincosamides, Streptogramine B antibiotics

Topics:

Foik IP, Tuszynska I, Feder M, Purta E, Stefaniak F, Bujnicki JM
Eur J Med Chem Volume 146, 25 February 2018, Pages 60-67 | DOI: 10.1016/j.ejmech.2017.11.032

IF: 4.519; 5-Year IF: 4.187

2018 RNArchitecture: a database and a classification system of RNA families, with a focus on structural information

Topics:

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
Nucleic Acids Res. 2018 Jan 4;46(D1):D202-D205. | DOI: 10.1093/nar/gkx966

IF: 10.162

2018 Exploring Baltic Sea cyanobacteria for small-molecule inhibitors of microRNA function: a project description

Topics:

Paweł Brzuzan, Hanna Mazur Marzec, Filip Stefaniak, Maciej Woźny, Maciej Florczyk
ENVIRONMENTAL BIOTECHNOLOGY 14 (1) 2018; Pages 1-4 | DOI: 10.14799/ebms301

2016 Molecularly Imprinted Polymer (MIP) Film with Improved Surface Area Developed by Using Metal-Organic Framework (MOF) for Sensitive Lipocalin (NGAL) Determination

Topics:

Zofia Iskierko, Piyush Sindhu Sharma, Daniel Prochowicz, Krzysztof Fronc, Francis D'Souza, Diana Toczydlowska, Filip Stefaniak, Krzysztof Noworyta
ACS Appl. Mater. Interfaces, 2016, 8 (31), pp 19860–19865 | DOI: 10.1021/acsami.6b05515

IF: 7.504

2015 Prediction of compounds activity in nuclear receptor signaling and stress pathway assays using machine learning algorithms and low dimensional molecular descriptors

Topics:

Filip Stefaniak
Front. Environ. Sci., 01 December 2015 | DOI: 10.3389/fenvs.2015.00077

IF: 4.581

2015 Modeling of ribonucleic acid–ligand interactions

Topics:

Filip Stefaniak, Ewa Chudyk (Joint First Authorship), Michael Bodkin, Wayne Dawson, Janusz M. Bujnicki
WIREs Comput Mol Sci 2015, 5:425–439. | DOI: 10.1002/wcms.1226

IF: 14.016

2015 Discovery of TRAF-2 and NCK-interacting kinase (TNIK) inhibitors by ligand-based virtual screening methods

Topics:

Anna Bujak, Filip Stefaniak (Joint First Authorship), Daria Zdzalik, Paulina Grygielewicz, Barbara Dymek, Marcin Zagozda, Pawel Gunerka, Monika Lamparska-Przybysz, Krzysztof Dubiel, Maciej Wieczoreka and Karolina Dzwonek
MedChemComm 6 (8), 2015, 1564-1572 | DOI: 10.1039/C5MD00090D

IF: 2.608