Publications

0000-0001-5758-9416
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Scopus ID: 14623077600 PBN - polon
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Generated on 2025-03-21

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

Topics:

Szulc N.A., Stefaniak F., Piechota M., Soszyńska A., Piórkowska G., Cappannini A., Bujnicki J.M., Maniaci C., and Pokrzywa W.
DEGRONOPEDIA: a web server for proteome-wide inspection of degrons
Nucleic Acids Research, Volume 52, Pages: W221-W232, 2024 | DOI: 10.1093/nar/gkae238

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

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

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

Topics:

Cappannini A., Ray A., Purta E., Mukherjee S., Boccaletto P., Moafinejad S.N., Lechner A., Barchet C., Klaholz B., Stefaniak F., and Bujnicki J.M.
MODOMICS: a database of RNA modifications and related information. 2023 update
Nucleic Acids Research, Volume 52, Issue D1, Pages: D239-D244, 2024 | 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 RNA-Puzzles Round V: blind predictions of 23 RNA structures

Topics:

Bu F., Adam Y., Adamiak R.W., Stefaniak F., and et al.
RNA-Puzzles Round V: blind predictions of 23 RNA structures
Nat Methods, Volume 22, Pages: 399-411, 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

Topics:

Moafinejad S.N., Aquino B.R.H., Boniecki M.J., Pandaranadar Jeyeram I.P.N., Nikolaev G., Magnus M., Amiri Farsani M., Badepally N.G., Wirecki T.K., Stefaniak F., and Bujnicki J.M.
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, Volume 52, Pages: W368-W373, 2024 | DOI: 10.1093/nar/gkae356

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

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

Topics:

Baulin E.F., Mukherjee S., Moafinejad S.N., Wirecki T.K., Badepally N.G., Jaryani F., Stefaniak F., Amiri Farsani M., Ray A., de Moura T.R., and Bujnicki J.M.
RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints
Proteins: Structure, Function, and Bioinformatics, Volume 91, Issue 12, Pages: 1800-1810, 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:

Szulc N.A., Mackiewicz Z., Bujnicki J.M., and Stefaniak F.
Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA
Briefings in Bioinformatics, 2023 | DOI: 10.1093/bib/bbad187

IF: 13.994

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 M., Zagozda M., Michałek S., Dymek B., Zdżalik-Bielecka D., Dziachan M., Orłowska N., Gunerka P., Turowski P., Hucz-Kalitowska J., Stańczak A., Stańczak P., Mulewski K., Smuga D., Stefaniak F., Gurba-Bryśkiewicz L., Leniak A., Ochal Z., Mach M., Dzwonek K., Lamparska-Przybysz M., Dubiel K., and Wieczorek M.
Design, Synthesis, and Development of pyrazolo[1,5-a]pyrimidine Derivatives as a Novel Series of Selective PI3Kδ Inhibitors: Part I—Indole Derivatives
Pharmaceuticals, Volume 15, Issue 8, Pages: 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:

Boccaletto P., Stefaniak F., Ray A., Cappannini A., Mukherjee S., Purta E., Kurkowska M., Shirvanizadeh N., Destefanis E., Groza P., Avşar G., Romitelli A., Pir P., Dassi E., Conticello S.G., Aguilo F., and Bujnicki J.M.
MODOMICS: a database of RNA modification pathways. 2021 update
Nucleic Acids Research, Volume 50, Issue D1, Pages: D231-D235, 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/

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

Topics:

Szulc N.A., Mackiewicz Z., Bujnicki J.M., and Stefaniak F.
fingeRNAt—A novel tool for high-throughput analysis of nucleic acid-ligand interactions
PLOS Computational Biology, Volume 18, Issue 6, Pages: e1009783, 2022 | DOI: 10.1371/journal.pcbi.1009783

IF: 4.779

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

Topics:

Ghosh P., Nithin C., Joshi A., Stefaniak F., Wirecki T.K., and Bujnicki J.M.
(book chapter) Computational Modeling Methods for 3D Structure Prediction of Ribozymes
Ribozymes, Volume 2, Pages: 861-881, 2021 | DOI: 10.1002/9783527814527.ch33

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

Topics:

Stefaniak F., and Bujnicki J.M.
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses
PLOS Computational Biology, 2021 | DOI: 10.1371/journal.pcbi.1008309

IF: 4.700

The AnnapuRNA repository: https://github.com/filipspl/AnnapuRNA

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

Topics:

Andryianau G., Kowalski M., Piotrowicz M.C., Rajkiewicz A.A., Dymek B., Sklepkiewicz P.L., Pluta E., Stefaniak F., Czestkowski W., Olejniczak S., Mazur M., Niedziejko P., Koralewski R., Matyszewski K., Gruza M., Zagozdzon A., Salamon M., Rymaszewska A., Welzer M., Dzwonek K., Golab J., Olczak J., Bartoszewicz A., and Golebiowski A.
Benzoxazepine-Derived Selective, Orally Bioavailable Inhibitor of Human Acidic Mammalian Chitinase
ACS Med. Chem. Lett., Volume 11, Issue 6, Pages: 1228-1235, 2020 | DOI: 10.1021/acsmedchemlett.0c00092

IF: 3.975 (2019)

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

Topics:

Brzuzan P., Mazur-Marzec H., Florczyk M., Stefaniak F., Fidor A., Konkel R., and Woźny M.
Luciferase reporter assay for small-molecule inhibitors of MIR92b-3p function: Screening cyanopeptolins produced by Nostoc from the Baltic Sea
Toxicology in Vitro, Volume 68, Pages: 104951, 2020 | 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:

Wirecki T.K., Merdas K., Bernat A., Boniecki M.J., Bujnicki J.M., and Stefaniak F.
RNAProbe: a web server for normalization and analysis of RNA structure probing data
Nucleic Acids Research, Volume 48, Issue W1, Pages: W292-W299, 2020 | DOI: 10.1093/nar/gkaa396

IF: 16.971; 5-Year IF: 15.542

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

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

Topics:

Ponce-Salvatierra A., Pluta R., Skowronek E., Orlowska M., Baginski B., Kurkowska M., Purta E., Ghosh P., Wirecki T., Stefaniak F., and Bujnicki JM.
(conference paper) Riboswitch-ligand structure determination using an integrative structural biology approach
FEBS OPEN BIO, Volume 9, Pages: 243-243, 2019

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

Topics:

Mazur M., Dymek B., Koralewski R., Sklepkiewicz P., Olejniczak S., Mazurkiewicz M., Piotrowicz M., Salamon M., Jędrzejczak K., Zagozdzon A., Czestkowski W., Matyszewski K., Borek B., Bartoszewicz A., Pluta E., Rymaszewska A., Mozga W., Stefaniak F., Dobrzański P., Dzwonek K., Golab J., Golebiowski A., and Olczak J.
Development of Dual Chitinase Inhibitors as Potential New Treatment for Respiratory System Diseases
Journal of Medicinal Chemistry, Volume 62, Issue 15, Pages: 7126-7145, 2019 | DOI: 10.1021/acs.jmedchem.9b00681

IF: 6.205 (2019)

2019 Structural bases of peptidoglycan recognition by lysostaphin SH3b domain

Topics:

Mitkowski P., Jagielska E., Nowak E., Bujnicki J.M., Stefaniak F., Niedziałek D., Bochtler M., and Sabała I.
Structural bases of peptidoglycan recognition by lysostaphin SH3b domain
Scientific Reports, Volume 9, Pages: 5965, 2019 | DOI: 10.1038/s41598-019-42435-z

IF: 4.122; 5-Year IF: 4.609

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 M.M., Dzwonek K., Golebiowski A., Golab J., and Olczak J.
Discovery of selective, orally bioavailable inhibitor of mouse chitotriosidase
Bioorg Med Chem Lett., Volume 28, Issue 3, Pages: 310-314, 2018 | DOI: 10.1016/j.bmcl.2017.12.047

IF: 2.454; 5-Year IF: 2.286

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

Topics:

Brzuzan P., Mazur-Marzec H., Stefaniak F., Woźny M., and Florczyk M.
Exploring Baltic Sea cyanobacteria for small-molecule inhibitors of microRNA function: a project description
ENVIRONMENTAL BIOTECHNOLOGY, Volume 14, Issue 1, Pages: 1-4, 2018 | DOI: 10.14799/ebms301

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

Topics:

Toczydlowska-Socha D., Zielinska M.M., Kurkowska M., Astha, Almeida C.F., Stefaniak F., Purta E., and Bujnicki J.M.
Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5′ termini
Phil. Trans. R. Soc. B, Volume 373, Pages: 20180161, 2018 | DOI: 10.1098/rstb.2018.0161

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

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

Topics:

Foik I.P., Tuszynska I., Feder M., Purta E., Stefaniak F., and Bujnicki J.M.
Novel inhibitors of the rRNA ErmC′ methyltransferase to block resistance to Macrolides, Lincosamides, Streptogramine B antibiotics
Eur J Med Chem, Volume 146, Pages: 60-67, 2018 | 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., and Bujnicki J.M.
RNArchitecture: a database and a classification system of RNA families, with a focus on structural information
Nucleic Acids Research, Volume 46, Issue D1, Pages: D202-D205, 2018 | DOI: 10.1093/nar/gkx966

IF: 10.162

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

Topics:

Moszczyński-Pętkowski R., Majer J., Borkowska M., Bojarski Ł., Janowska S., Matłoka M., Stefaniak F., Smuga D., Bazydło K., Dubiel K., and Wieczorek M.
Synthesis and characterization of novel classes of PDE10A inhibitors - 1H-1,3-benzodiazoles and imidazo[1,2-a]pyrimidines
European Journal of Medicinal Chemistry, Volume 155, Pages: 96-116, 2018 | DOI: 10.1016/j.ejmech.2018.05.043

IF: 4.519; 5-Year IF: 4.187

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

Topics:

Iskierko Z., Sharma P.S., Prochowicz D., Fronc K., D'Souza F., Toczydlowska D., Stefaniak F., and Noworyta K.
Molecularly Imprinted Polymer (MIP) Film with Improved Surface Area Developed by Using Metal-Organic Framework (MOF) for Sensitive Lipocalin (NGAL) Determination
ACS Appl. Mater. Interfaces, Volume 8, Issue 31, Pages: 19860-19865, 2016 | DOI: 10.1021/acsami.6b05515

IF: 7.504

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

Topics:

Bujak A., Stefaniak F., Zdzalik D., Grygielewicz P., Dymek B., Zagozda M., Gunerka P., Lamparska-Przybysz M., Dubiel K., Wieczorek M., and Dzwonek K.
Discovery of TRAF-2 and NCK-interacting kinase (TNIK) inhibitors by ligand-based virtual screening methods
MedChemComm, Volume 6, Issue 8, Pages: 1564-1572, 2015 | DOI: 10.1039/C5MD00090D

IF: 2.608

2015 Modeling of ribonucleic acid–ligand interactions

Topics:

Stefaniak F., Chudyk E., Bodkin M., Dawson W., and Bujnicki J.M.
Modeling of ribonucleic acid–ligand interactions
WIREs Comput Mol Sci, Volume 5, Pages: 425-439, 2015 | DOI: 10.1002/wcms.1226

IF: 14.016

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

Topics:

Stefaniak F.
Prediction of compounds activity in nuclear receptor signaling and stress pathway assays using machine learning algorithms and low dimensional molecular descriptors
Front. Environ. Sci., 2015 | DOI: 10.3389/fenvs.2015.00077

IF: 4.581