Janusz M Bujnicki (Janusz Bujnicki)

Scopus Author ID ORCID

Publication Activity (10 Years)

Years Active: 2014-2024
Publications (10 Years): 32

Top Topics

Structural Basis

Artificial Intelligence

Molecular Dynamics

Top Venues

Nucleic acids research

RNA (New York, N.Y.)

PLoS computational biology

This page only lists publications with an associated author ORCID identifier.

Publications

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)
Tales Rocha de Moura, Elzbieta Purta, Agata Bernat, Eva M Martín-Cuevas, Małgorzata Kurkowska, Eugene F Baulin, Sunandan Mukherjee, Jakub Nowak, Artur P Biela, Michal Rawski, Sebastian Glatt, Fernando Moreno-Herrero, Janusz M Bujnicki
Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes. Nucleic acids research (2024)
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 52 (W1) (2024)
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 52 (W1) (2024)
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 52 (W1) (2024)
Tales Rocha de Moura, Elzbieta Purta, Agata Bernat, Eva M Martín-Cuevas, Małgorzata Kurkowska, Eugene F Baulin, Sunandan Mukherjee, Jakub Nowak, Artur P Biela, Michal Rawski, Sebastian Glatt, Fernando Moreno-Herrero, Janusz M Bujnicki
Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes. Nucleic acids research 52 (6) (2024)
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)
Davyd R Bohdan, Janusz M Bujnicki, Eugene F Baulin
ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment. Nucleic acids research (2024)
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)
Tales Rocha de Moura, Elzbieta Purta, Agata Bernat, Eva M Martín-Cuevas, Małgorzata Kurkowska, Eugene F Baulin, Sunandan Mukherjee, Jakub Nowak, Artur P Biela, Michal Rawski, Sebastian Glatt, Fernando Moreno-Herrero, Janusz M Bujnicki
Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes. Nucleic acids research 52 (6) (2024)
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 52 (W1) (2024)
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 52 (W1) (2024)
Tales Rocha de Moura, Elzbieta Purta, Agata Bernat, Eva M Martín-Cuevas, Małgorzata Kurkowska, Eugene F Baulin, Sunandan Mukherjee, Jakub Nowak, Artur P Biela, Michal Rawski, Sebastian Glatt, Fernando Moreno-Herrero, Janusz M Bujnicki
Conserved structures and dynamics in 5'-proximal regions of Betacoronavirus RNA genomes. Nucleic acids research 52 (6) (2024)
Andrea Cappannini, Angana Ray, Elzbieta Purta, Sunandan Mukherjee, Pietro Boccaletto, S Naeim Moafinejad, Antony Lechner, Charles Barchet, Bruno P Klaholz, Filip Stefaniak, Janusz M Bujnicki
MODOMICS: a database of RNA modifications and related information. 2023 update. Nucleic acids research (2023)
Rachael C Kretsch, Ebbe Sloth Andersen, Janusz M Bujnicki, Wah Chiu, Rachel J Hagey, Bingnan Luo, Benoît Masquida, Ewan K S McRae, Griffin M Schroeder, Zhaoming Su, Joseph E Wedekind, Lily Xu, Kaiming Zhang, Ivan N Zheludev, John Moult, Andriy Kryshtafovych
RNA target highlights in CASP15: Evaluation of predicted models by structure providers. Proteins (2023)
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 (2023)
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) (2022)
Julita Gumna, Maciej Antczak, Ryszard W Adamiak, Janusz M Bujnicki, Shi-Jie Chen, Feng Ding, Pritha Ghosh, Jun Li, Sunandan Mukherjee, Chandran Nithin, Katarzyna Pachulska-Wieczorek, Almudena Ponce-Salvatierra, Mariusz Popenda, Joanna Sarzyńska, Tomasz K Wirecki, Dong Zhang, Sicheng Zhang, Tomasz Zok, Eric Westhof, Zhichiao Miao, Marta Szachniuk, Agnieszka Rybarczyk
Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models. International journal of molecular sciences 23 (17) (2022)
S Naeim Moafinejad, Iswarya Pandara Nayaka Pj, Farhang Jaryani, Niloofar Shirvanizadeh, Eugene Baulin, Janusz M Bujnicki
1D2DSimScore: A novel method for comparing contacts in biomacromolecules and their complexes. Protein science : a publication of the Protein Society (2022)
Natalia Koralewska, Agnieszka Szczepanska, Kinga Ciechanowska, Marta Wojnicka, Maria Pokornowska, Marek C Milewski, Dorota Gudanis, Daniel Baranowski, Chandran Nithin, Janusz M Bujnicki, Zofia Gdaniec, Marek Figlerowicz, Anna Kurzynska-Kokorniak
RNA and DNA G-quadruplexes bind to human dicer and inhibit its activity. Cellular and molecular life sciences : CMLS 78 (7) (2021)
Pietro Boccaletto, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Elzbieta Purta, Małgorzata Kurkowska, Niloofar Shirvanizadeh, Eliana Destefanis, Paula Groza, Gülben Avşar, Antonia Romitelli, Pınar Pir, Erik Dassi, Silvestro Giovanni Conticello, Francesca Aguilo, Janusz M Bujnicki
MODOMICS: a database of RNA modification pathways. 2021 update. Nucleic acids research (2021)
Filip Stefaniak, Janusz M Bujnicki
AnnapuRNA: A scoring function for predicting RNA-small molecule binding poses. PLoS computational biology 17 (2) (2021)
Zhichiao Miao, Ryszard W Adamiak, Maciej Antczak, Michał J Boniecki, Janusz M Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Yi Cheng, Fang-Chieh Chou, Rachel J Hagey, Nikolay V Dokholyan, Feng Ding, Caleb Geniesse, Yangwei Jiang, Astha Joshi, Andrey Krokhotin, Marcin Magnus, Olivier Mailhot, Francois Major, Thomas H Mann, Paweł Piątkowski, Radoslaw Pluta, Mariusz Popenda, Joanna Sarzyńska, Lizhen Sun, Marta Szachniuk, Siqi Tian, Jian Wang, Jun Wang, Andrew M Watkins, Jakub Wiedemann, Yi Xiao, Xiaojun Xu, Joseph D Yesselman, Dong Zhang, Yi Zhang, Zhenzhen Zhang, Chenhan Zhao, Peinan Zhao, Yuanzhe Zhou, Tomasz Zok, Adriana Żyła, Aiming Ren, Robert T Batey, Barbara L Golden, Lin Huang, David M J Lilley, Yijin Liu, Dinshaw J Patel, Eric Westhof
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA (New York, N.Y.) 26 (8) (2020)
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 9 (1) (2019)
Almudena Ponce-Salvatierra, Astha Joshi, Katarzyna Merdas, Chandran Nithin, Pritha Ghosh, Sunandan Mukherjee, Janusz M Bujnicki
Computational modeling of RNA 3D structure based on experimental data. Bioscience reports 39 (2) (2019)
Michael F Jantsch, Alessandro Quattrone, Mary O'Connell, Mark Helm, Michaela Frye, Manuel Macias-Gonzales, Marie Ohman, Stefan Ameres, Luc Willems, Francois Fuks, Anastasis Oulas, Stepanka Vanacova, Henrik Nielsen, Cecile Bousquet-Antonelli, Yuri Motorin, Jean-Yves Roignant, Nikolaos Balatsos, Andras Dinnyes, Pavel Baranov, Vincent Kelly, Ayelet Lamm, Gideon Rechavi, Mattia Pelizzola, Janis Liepins, Irina Holodnuka Kholodnyuk, Vanessa Zammit, Duncan Ayers, Finn Drablos, John Arne Dahl, Janusz M Bujnicki, Carmen Jerónimo, Raquel Almeida, Monica Neagu, Marieta Costache, Jasna Bankovic, Bojana Banovic, Jan Kyselovic, Luis Miguel Valor, Stefan Selbert, Pinar Pir, Turan Demircan, Victoria Cowling, Matthias R Schaefer, Walter Rossmanith, Denis Lafontaine, Alexandre David, Clement Carre, Frank Lyko, Raffael Schaffrath, Schraga Schwartz, Andre Verdel, Arne Klungland, Elzbieta Purta, Gordana Timotijevic, Fernando Cardona, Alberto Davalos, Ester Ballana, Donal O Carroll, Jernej Ule, Rupert Fray
Positioning Europe for the EPITRANSCRIPTOMICS challenge. RNA biology 15 (6) (2018)
Diana Toczydlowska-Socha, Magdalena M Zielinska, Malgorzata Kurkowska, Astha Joshi, Catarina F Almeida, Filip Stefaniak, Elzbieta Purta, Janusz M Bujnicki
Human RNA cap1 methyltransferase CMTr1 cooperates with RNA helicase DHX15 to modify RNAs with highly structured 5' termini. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 373 (1762) (2018)
Humberto Fernandes, Honorata Czapinska, Katarzyna Grudziaz, Janusz M Bujnicki, Martyna Nowacka
Crystal structure of human Acinus RNA recognition motif domain. PeerJ 6 (2018)
Pooja Kumari, Florian Aeschimann, Dimos Gaidatzis, Jeremy J Keusch, Pritha Ghosh, Anca Neagu, Katarzyna Pachulska-Wieczorek, Janusz M Bujnicki, Heinz Gut, Helge Großhans, Rafal Ciosk
Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition. Nature communications 9 (1) (2018)
Lucyna Budzko, Paulina Jackowiak, Karol Kamel, Joanna Sarzynska, Janusz M Bujnicki, Marek Figlerowicz
Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro. Scientific reports 7 (1) (2017)
Zhichiao Miao, Ryszard W Adamiak, Maciej Antczak, Robert T Batey, Alexander J Becka, Marcin Biesiada, Michał J Boniecki, Janusz M Bujnicki, Shi-Jie Chen, Clarence Yu Cheng, Fang-Chieh Chou, Adrian R Ferré-D'Amaré, Rhiju Das, Wayne K Dawson, Feng Ding, Nikolay V Dokholyan, Stanisław Dunin-Horkawicz, Caleb Geniesse, Kalli Kappel, Wipapat Kladwang, Andrey Krokhotin, Grzegorz E Łach, François Major, Thomas H Mann, Marcin Magnus, Katarzyna Pachulska-Wieczorek, Dinshaw J Patel, Joseph A Piccirilli, Mariusz Popenda, Katarzyna J Purzycka, Aiming Ren, Greggory M Rice, John Santalucia, Joanna Sarzyńska, Marta Szachniuk, Arpit Tandon, Jeremiah J Trausch, Siqi Tian, Jian Wang, Kevin M Weeks, Benfeard Williams, Yi Xiao, Xiaojun Xu, Dong Zhang, Tomasz Zok, Eric Westhof
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA (New York, N.Y.) 23 (5) (2017)
Marcin Magnus, Michał J Boniecki, Wayne Dawson, Janusz M Bujnicki
SimRNAweb: a web server for RNA 3D structure modeling with optional restraints. Nucleic acids research 44 (W1) (2016)
Bart Van Laer, Martine Roovers, Lina Wauters, Joanna M Kasprzak, Michal Dyzma, Egon Deyaert, Ranjan Kumar Singh, André Feller, Janusz M Bujnicki, Louis Droogmans, Wim Versées
Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue. Nucleic acids research 44 (2) (2015)
Irina Tuszynska, Marcin Magnus, Katarzyna Jonak, Wayne Dawson, Janusz M Bujnicki
NPDock: a web server for protein-nucleic acid docking. Nucleic acids research 43 (W1) (2015)
Dawid Głów, Dariusz Pianka, Agata A Sulej, Łukasz P Kozłowski, Justyna Czarnecka, Grzegorz Chojnowski, Krzysztof J Skowronek, Janusz M Bujnicki
Sequence-specific cleavage of dsRNA by Mini-III RNase. Nucleic acids research 43 (5) (2015)
Heping Zheng, Ivan G Shabalin, Katarzyna B Handing, Janusz M Bujnicki, Wladek Minor
Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection. Nucleic acids research 43 (7) (2015)
Michal J Boniecki, Grzegorz Lach, Wayne K Dawson, Konrad Tomala, Pawel Lukasz, Tomasz Soltysinski, Kristian M Rother, Janusz M Bujnicki
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction. Nucleic acids research 44 (7) (2015)
Mohit Chawla, Romina Oliva, Janusz M Bujnicki, Luigi Cavallo
An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies. Nucleic acids research 43 (14) (2015)
Tomasz Waleń, Grzegorz Chojnowski, Przemysław Gierski, Janusz M Bujnicki
ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes. Nucleic acids research 42 (19) (2014)
Karolina Mierzejewska, Wojciech Siwek, Honorata Czapinska, Magdalena Kaus-Drobek, Monika Radlinska, Krzysztof Skowronek, Janusz M Bujnicki, Michal Dadlez, Matthias Bochtler
Structural basis of the methylation specificity of R.DpnI. Nucleic acids research 42 (13) (2014)