1.

RNA-Puzzles Round V: Blind predictions of 23 RNA structures / Fan Bu, Yagoub Adam, R. W. Adamiak (WIiT), Maciej Antczak (WIiT), Belisa Rebeca H. De Aquino, Nagendar Goud Badepally, Robert T. Batey, Eugene F. Baulin, Paweł Boiński (WIiT), Michal J. Boniecki, Janusz M. Bujnicki, Kristy A. Carpenter, Jose Chacon, Shi-Jie Chen, Wah Chiu, Pablo Cordero, Naba Krishna Das, Rhiju Das, Wayne K. Dawson, Frank Dimaio, Feng Ding, Anne-Catherine Dock-Bregeon, Nikolay V. Dokholyan, Ron O. Dror, Stanisław Dunin-Horkawicz, Stephan Eismann, Eric Ennifar, Reza Esmaeeli, Masoud Amiri Farsani, Adrian R. Ferré-D’amaré, Caleb Geniesse, George E. Ghanim, Horacio V. Guzman, Iris V. Hood, Lin Huang, Dharm Skandh Jain, Farhang Jaryani, Lei Jin, Astha Joshi, Masha Karelina, Jeffrey S. Kieft, Wipapat Kladwang, Sebastian Kmiecik, Deepak Koirala, Markus Kollmann, Rachael C. Kretsch, Mateusz Kruciński, Jun Li, Shuang Li, Marcin Magnus, Benoît Masquida, S. Naeim Moafinejad, Arup Mondal, Sunandan Mukherjee, Thi Hoang Duong Nguyen, Grigory Nikolaev, Chandran Nithin, Grace Nye, Iswarya P. N. Pandaranadar Jeyeram, Alberto Perez, Phillip Pham, Joseph A. Piccirilli, Smita Priyadarshini Pilla, Radosław Pluta, Simón Poblete, Almudena Ponce-Salvatierra, Mariusz Popenda, Lukasz Popenda, Fabrizio Pucci, Ramya Rangan, Angana Ray, Aiming Ren, Joanna Sarzynska, Congzhou Mike Sha, Filip Stefaniak, Zhaoming Su, Krishna C. Suddala, Marta Szachniuk (WIiT), Raphael Townshend, Robert J. Trachman Iii, Jian Wang, Wenkai Wang, Andrew Watkins, Tomasz K. Wirecki, Yi Xiao, Peng Xiong, Yiduo Xiong, Jianyi Yang, Joseph David Yesselman, Jinwei Zhang, Yi Zhang, Zhenzhen Zhang, Yuanzhe Zhou, Tomasz Żok (WIiT), Dong Zhang, Sicheng Zhang, Adriana Żyła, Eric Westhof, Zhichao Miao // Nature Methods - 2025, vol. 22, p. 399-411

Scientific article 200 36,1

2.

Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models / Julita Gumna, Maciej Antczak (WIiT), Ryszard W. Adamiak (WIiT), 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 Wirecki, Dong Zhang, Sicheng Zhang, Tomasz Żok (WIiT), Eric Westhof, Zhichao Miao, Marta Szachniuk (WIiT), Agnieszka Rybarczyk (WIiT) // International Journal of Molecular Sciences - 2022, vol. 23, iss. 17, p. 9630-1-9630-20

Scientific article 140 5,6

3.

Entanglements of structure elements revealed in RNA 3D models / Mariusz Popenda, Tomasz Żok (WIiT), Joanna Sarzyńska, Agnieszka Korpeta, Ryszard W. Adamiak, Maciej Antczak, Marta Szachniuk (WIiT) // Nucleic Acids Research - 2021, vol. 49, iss. 17, p. 9625-9632

Scientific article 200 19,16

4.

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers / Zhichao Miao, Ryszard Adamiak, Maciej Antczak (WIiT), Michał Boniecki, Janusz M. Bujnicki, Shi-Jie Chen, Clarence Y. Cheng, Yi Cheng, Fang-Chieh Chou, Rhiju Das, Nikolay V. Dokholyan, Feng Ding, Caleb Geniesse, Yangwei Jiang, Astha Joshi, Andrey Krokhotin, Marcin Magnus, Olivier Mailhot, Francois Major, Thomas H. Mann, Paweł Piątkowski, Radosław Pluta, Mariusz Popenda, Joanna Sarzyńska, Lizhen Sun, Marta Szachniuk (WIiT), Sigi Tian, Jian Wang, Andrew M. Watkins, Jakub Wiedemann (WIiT), Xiaojun Xu, Joseph D. Yesselman, Dong Zhang, Zhenzhen Zhang, Chenhan Zhao, Peinan Zhao, Yuanzhe Zhou, Tomasz Żok (WIiT), Adriana Żyła, Aiming Ren, Robert T. Batey, Barbara L. Golden, Lin Huang, David M. Lilley, Yijin Liu, Dinshaw J. Patel, Eric Westhof // RNA - 2020, vol. 26, no. 12, p. 982-995

Scientific article 140 4,942

5.

New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation / Maciej Antczak (WI), Mariusz Popenda, Tomasz Żok (WI), Michał Żurkowski (WI), Ryszard W. Adamiak, Marta Szachniuk // Bioinformatics - 2018, vol. 34, iss. 8, p. 1304-1312

Scientific article 45 4,531

6.

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures / Maciej Antczak (WI), Tomasz Żok (WI), Maciej Osowiecki, Mariusz Popenda, Ryszard Adamiak (WI), Marta Szachniuk // BMC Bioinformatics - 2018, vol. 19, p. 1-11

Scientific article 35 2,511

7.

RNApdbee 2.0: multifunctional tool for RNA structure annotation / Tomasz Żok (WI), Maciej Antczak (WI), Michał Żurkowski (WI), Mariusz Popenda, Jacek Błażewicz (WI), Ryszard Adamiak, Marta Szachniuk // Nucleic Acids Research - 2018, vol. 46, iss. Web Server, p. W30-W35

Scientific article 40 11,147

8.

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme / Z. Miao, Ryszard Adamiak (WI), Maciej Antczak (WI), Robert Batey, Alexander Becka, Marcin Biesiada, M. Boniecki, Janusz M. Bujnicki, S. J. Chen, C. Cheng, F. C. Chou, A. R. Ferre-D'Amare, R. Das, Wayne Dawson, F. Ding, N. V. Dokholyan, S. Dunin-Horkawicz, C. Geniesse, Kalli Kappel, W. Kladwang, A. Krokhotin, G. Lach, F. Major, T. H. Mann, M. Magnus, Katarzyna Pachulska-Wieczorek, Dinshaw Patel, Joseph Piccirilli, Mariusz Popenda, Katarzyna J. Purzycka, Aiming Ren, Gregorry Rice, John Santalucia, Joanna Sarzyńska, Marta Szachniuk (WI), A. Tandon, Jeremiah Trausch, S. Tian, J. Wang, Kevin Weeks, Benfeard Williams, Y. Xiao, X. Xu, Dong Zhang, Tomasz Żok (WI), E. Westhof // RNA - 2017, vol. 23, no. 5, p. 655-672

Scientific article 35 4,49

9.

New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure / Maciej Antczak (WI), Mariusz Popenda, Tomasz Żok (WI), Joanna Sarzyńska, Tomasz Ratajczak (WI), Katarzyna Tomczyk (WI), Ryszard W. Adamiak, Marta Szachniuk (WI) // Acta Biochimica Polonica - 2016, vol. 63, no. 4, p. 737-744

Scientific article 15 1,159

10.

Automated 3D RNA structure prediction using the RNAComposer method for riboswitches / K. J. Purzycka, M. Popenda, Marta Szachniuk, Maciej Antczak (WI), Piotr Łukasiak, Jacek Błażewicz, R. W. Adamiak // Methods in Enzymology - 2015, vol. 553, p. 3-34

Scientific article 25

11.

New in silico approach to assessing RNA secondary structures with non-canonical base pairs / Agnieszka Rybarczyk, Natalia Szóstak, Maciej Antczak (WI), Tomasz Żok (WI), Mariusz Popenda, Ryszard Adamiak, Jacek Błażewicz (WI), Marta Szachniuk // BMC Bioinformatics - 2015, vol. 16, p. 276-1-276-12

Scientific article 35 2,435

12.

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures / Z. Miao, R. W. Adamiak, M F. Blanchet, M. Boniecki, J. M. Bujnicki, S. J. Chen, C. Cheng, G. Chojnowski, F. C. Chou, P. Cordero, J. A. Cruz, A. R. Ferre-D'Amare, F. Ding, R. Das, N. V. Dokholyan, S. Dunin-Horkawicz, W. Kladwang, A. Krokhotin, G. Lach, M. Magnus, F. Major, T. H. Mann, B. Masquida, D. Matelska, M. Meyer, A. Peselis, M. Popenda, K. J. Purzycka, A. Serganov, J. Stasiewicz, Marta Szachniuk (WI), A. Tandon, S. Tian, J. Wang, Y. Xiao, X. Xu, J. Zhang, P. Zhao, Tomasz Żok (WI), E. Westhof // RNA - 2015, vol. 21, no. 6, p. 1066-1084

Scientific article 35

13.

RNAssess - a web server for quality assessment of RNA 3D structures / Piotr Łukasiak, Maciej Antczak (WI), Tomasz Ratajczak (WI), Marta Szachniuk, Mariusz Popenda, Ryszard Adamiak (WI), Jacek Błażewicz (WI) // Nucleic Acids Research - 2015, vol. 43, no. W1, p. W502-W-506

Scientific article 40 9,202

14.

RNApdbee - a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs / Maciej Antczak (WI), Tomasz Żok (WI), Mariusz Popenda, Piotr Łukasiak (WI), Ryszard W. Adamiak (WI), Jacek Błażewicz (WI), Marta Szachniuk // Nucleic Acids Research - 2014, vol. 42, iss. W1, p. W368-W372

Scientific article 40 9,112

15.

RNAlyzer-novel approach for quality analysis of RNA structural models / Piotr Łukasiak, Maciej Antczak (WI), Tomasz Ratajczak (WI), Janusz M. Bujnicki, Marta Szachniuk, Ryszard W. Adamiak, Mariusz Popenda, Jacek Błażewicz // Nucleic Acids Research - 2013, vol. 41, iss. 12, p. 5978-5990

Scientific article 40 8,808

16.

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures / M. Popenda, M. Błażewicz, Marta Szachniuk, R. W. Adamiak // Nucleic Acids Research - 2008, iss. suppl. 1, p. D386-D391

Scientific article 6,878