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RNA-Puzzles Round V: blind predictions of 23 RNA structures.

Fuente: PubMed

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Autori principali:	Bu, Fan, Adam, Yagoub, Adamiak, Ryszard W, Antczak, Maciej, de Aquino, Belisa Rebeca H, Badepally, Nagendar Goud, Batey, Robert T, Baulin, Eugene F, Boinski, Pawel, Boniecki, Michal J, Bujnicki, Janusz M, Carpenter, Kristy A, Chacon, Jose, Chen, Shi-Jie, Chiu, Wah, Cordero, Pablo, Das, Naba Krishna, Das, Rhiju, Dawson, Wayne K, DiMaio, Frank, Ding, Feng, Dock-Bregeon, Anne-Catherine, Dokholyan, Nikolay V, Dror, Ron O, Dunin-Horkawicz, Stanisław, Eismann, Stephan, Ennifar, Eric, Esmaeeli, Reza, Farsani, Masoud Amiri, Ferré-D'Amaré, Adrian R, Geniesse, Caleb, Ghanim, George E, Guzman, Horacio V, Hood, Iris V, Huang, Lin, Jain, Dharm Skandh, Jaryani, Farhang, Jin, Lei, Joshi, Astha, Karelina, Masha, Kieft, Jeffrey S, Kladwang, Wipapat, Kmiecik, Sebastian, Koirala, Deepak, Kollmann, Markus, Kretsch, Rachael C, Kurciński, Mateusz, Li, Jun, Li, Shuang, Magnus, Marcin, Masquida, BenoÎt, Moafinejad, S Naeim, Mondal, Arup, Mukherjee, Sunandan, Nguyen, Thi Hoang Duong, Nikolaev, Grigory, Nithin, Chandran, Nye, Grace, Pandaranadar Jeyeram, Iswarya P N, Perez, Alberto, Pham, Phillip, Piccirilli, Joseph A, Pilla, Smita Priyadarshini, Pluta, Radosław, Poblete, Simón, Ponce-Salvatierra, Almudena, Popenda, Mariusz, Popenda, Lukasz, Pucci, Fabrizio, Rangan, Ramya, Ray, Angana, Ren, Aiming, Sarzynska, Joanna, Sha, Congzhou Mike, Stefaniak, Filip, Su, Zhaoming, Suddala, Krishna C, Szachniuk, Marta, Townshend, Raphael, Trachman, Robert J, Wang, Jian, Wang, Wenkai, Watkins, Andrew, Wirecki, Tomasz K, Xiao, Yi, Xiong, Peng, Xiong, Yiduo, Yang, Jianyi, Yesselman, Joseph David, Zhang, Jinwei, Zhang, Yi, Zhang, Zhenzhen, Zhou, Yuanzhe, Zok, Tomasz, Zhang, Dong, Zhang, Sicheng, Żyła, Adriana, Westhof, Eric, Miao, Zhichao
Natura:	Artículo científico
Lingua:	en
Pubblicazione:	Nature methods 2025
Soggetti:	RNA Nucleic Acid Conformation Models, Molecular Computational Biology RNA, Catalytic Aptamers, Nucleotide
Accesso online:	Acceder al recurso
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author	Bu, Fan Adam, Yagoub Adamiak, Ryszard W Antczak, Maciej de Aquino, Belisa Rebeca H Badepally, Nagendar Goud Batey, Robert T Baulin, Eugene F Boinski, Pawel Boniecki, Michal J Bujnicki, Janusz M Carpenter, Kristy A Chacon, Jose Chen, Shi-Jie Chiu, Wah Cordero, Pablo Das, Naba Krishna Das, Rhiju Dawson, Wayne K DiMaio, Frank Ding, Feng Dock-Bregeon, Anne-Catherine Dokholyan, Nikolay V Dror, Ron O Dunin-Horkawicz, Stanisław Eismann, Stephan Ennifar, Eric Esmaeeli, Reza Farsani, Masoud Amiri Ferré-D'Amaré, Adrian R Geniesse, Caleb Ghanim, George E Guzman, Horacio V Hood, Iris V Huang, Lin Jain, Dharm Skandh Jaryani, Farhang Jin, Lei Joshi, Astha Karelina, Masha Kieft, Jeffrey S Kladwang, Wipapat Kmiecik, Sebastian Koirala, Deepak Kollmann, Markus Kretsch, Rachael C Kurciński, Mateusz Li, Jun Li, Shuang Magnus, Marcin Masquida, BenoÎt Moafinejad, S Naeim Mondal, Arup Mukherjee, Sunandan Nguyen, Thi Hoang Duong Nikolaev, Grigory Nithin, Chandran Nye, Grace Pandaranadar Jeyeram, Iswarya P N Perez, Alberto Pham, Phillip Piccirilli, Joseph A Pilla, Smita Priyadarshini Pluta, Radosław Poblete, Simón Ponce-Salvatierra, Almudena Popenda, Mariusz Popenda, Lukasz Pucci, Fabrizio Rangan, Ramya Ray, Angana Ren, Aiming Sarzynska, Joanna Sha, Congzhou Mike Stefaniak, Filip Su, Zhaoming Suddala, Krishna C Szachniuk, Marta Townshend, Raphael Trachman, Robert J Wang, Jian Wang, Wenkai Watkins, Andrew Wirecki, Tomasz K Xiao, Yi Xiong, Peng Xiong, Yiduo Yang, Jianyi Yesselman, Joseph David Zhang, Jinwei Zhang, Yi Zhang, Zhenzhen Zhou, Yuanzhe Zok, Tomasz Zhang, Dong Zhang, Sicheng Żyła, Adriana Westhof, Eric Miao, Zhichao
author_facet	Bu, Fan Adam, Yagoub Adamiak, Ryszard W Antczak, Maciej de Aquino, Belisa Rebeca H Badepally, Nagendar Goud Batey, Robert T Baulin, Eugene F Boinski, Pawel Boniecki, Michal J Bujnicki, Janusz M Carpenter, Kristy A Chacon, Jose Chen, Shi-Jie Chiu, Wah Cordero, Pablo Das, Naba Krishna Das, Rhiju Dawson, Wayne K DiMaio, Frank Ding, Feng Dock-Bregeon, Anne-Catherine Dokholyan, Nikolay V Dror, Ron O Dunin-Horkawicz, Stanisław Eismann, Stephan Ennifar, Eric Esmaeeli, Reza Farsani, Masoud Amiri Ferré-D'Amaré, Adrian R Geniesse, Caleb Ghanim, George E Guzman, Horacio V Hood, Iris V Huang, Lin Jain, Dharm Skandh Jaryani, Farhang Jin, Lei Joshi, Astha Karelina, Masha Kieft, Jeffrey S Kladwang, Wipapat Kmiecik, Sebastian Koirala, Deepak Kollmann, Markus Kretsch, Rachael C Kurciński, Mateusz Li, Jun Li, Shuang Magnus, Marcin Masquida, BenoÎt Moafinejad, S Naeim Mondal, Arup Mukherjee, Sunandan Nguyen, Thi Hoang Duong Nikolaev, Grigory Nithin, Chandran Nye, Grace Pandaranadar Jeyeram, Iswarya P N Perez, Alberto Pham, Phillip Piccirilli, Joseph A Pilla, Smita Priyadarshini Pluta, Radosław Poblete, Simón Ponce-Salvatierra, Almudena Popenda, Mariusz Popenda, Lukasz Pucci, Fabrizio Rangan, Ramya Ray, Angana Ren, Aiming Sarzynska, Joanna Sha, Congzhou Mike Stefaniak, Filip Su, Zhaoming Suddala, Krishna C Szachniuk, Marta Townshend, Raphael Trachman, Robert J Wang, Jian Wang, Wenkai Watkins, Andrew Wirecki, Tomasz K Xiao, Yi Xiong, Peng Xiong, Yiduo Yang, Jianyi Yesselman, Joseph David Zhang, Jinwei Zhang, Yi Zhang, Zhenzhen Zhou, Yuanzhe Zok, Tomasz Zhang, Dong Zhang, Sicheng Żyła, Adriana Westhof, Eric Miao, Zhichao Bu, Fan Adam, Yagoub Adamiak, Ryszard W Antczak, Maciej de Aquino, Belisa Rebeca H Badepally, Nagendar Goud Batey, Robert T Baulin, Eugene F Boinski, Pawel Boniecki, Michal J Bujnicki, Janusz M Carpenter, Kristy A Chacon, Jose Chen, Shi-Jie Chiu, Wah Cordero, Pablo Das, Naba Krishna Das, Rhiju Dawson, Wayne K DiMaio, Frank Ding, Feng Dock-Bregeon, Anne-Catherine Dokholyan, Nikolay V Dror, Ron O Dunin-Horkawicz, Stanisław Eismann, Stephan Ennifar, Eric Esmaeeli, Reza Farsani, Masoud Amiri Ferré-D'Amaré, Adrian R Geniesse, Caleb Ghanim, George E Guzman, Horacio V Hood, Iris V Huang, Lin Jain, Dharm Skandh Jaryani, Farhang Jin, Lei Joshi, Astha Karelina, Masha Kieft, Jeffrey S Kladwang, Wipapat Kmiecik, Sebastian Koirala, Deepak Kollmann, Markus Kretsch, Rachael C Kurciński, Mateusz Li, Jun Li, Shuang Magnus, Marcin Masquida, BenoÎt Moafinejad, S Naeim Mondal, Arup Mukherjee, Sunandan Nguyen, Thi Hoang Duong Nikolaev, Grigory Nithin, Chandran Nye, Grace Pandaranadar Jeyeram, Iswarya P N Perez, Alberto Pham, Phillip Piccirilli, Joseph A Pilla, Smita Priyadarshini Pluta, Radosław Poblete, Simón Ponce-Salvatierra, Almudena Popenda, Mariusz Popenda, Lukasz Pucci, Fabrizio Rangan, Ramya Ray, Angana Ren, Aiming Sarzynska, Joanna Sha, Congzhou Mike Stefaniak, Filip Su, Zhaoming Suddala, Krishna C Szachniuk, Marta Townshend, Raphael Trachman, Robert J Wang, Jian Wang, Wenkai Watkins, Andrew Wirecki, Tomasz K Xiao, Yi Xiong, Peng Xiong, Yiduo Yang, Jianyi Yesselman, Joseph David Zhang, Jinwei Zhang, Yi Zhang, Zhenzhen Zhou, Yuanzhe Zok, Tomasz Zhang, Dong Zhang, Sicheng Żyła, Adriana Westhof, Eric Miao, Zhichao
collection	PubMed - marine biology
contents	RNA-Puzzles Round V: blind predictions of 23 RNA structures. Bu, Fan Adam, Yagoub Adamiak, Ryszard W Antczak, Maciej de Aquino, Belisa Rebeca H Badepally, Nagendar Goud Batey, Robert T Baulin, Eugene F Boinski, Pawel Boniecki, Michal J Bujnicki, Janusz M Carpenter, Kristy A Chacon, Jose Chen, Shi-Jie Chiu, Wah Cordero, Pablo Das, Naba Krishna Das, Rhiju Dawson, Wayne K DiMaio, Frank Ding, Feng Dock-Bregeon, Anne-Catherine Dokholyan, Nikolay V Dror, Ron O Dunin-Horkawicz, Stanisław Eismann, Stephan Ennifar, Eric Esmaeeli, Reza Farsani, Masoud Amiri Ferré-D'Amaré, Adrian R Geniesse, Caleb Ghanim, George E Guzman, Horacio V Hood, Iris V Huang, Lin Jain, Dharm Skandh Jaryani, Farhang Jin, Lei Joshi, Astha Karelina, Masha Kieft, Jeffrey S Kladwang, Wipapat Kmiecik, Sebastian Koirala, Deepak Kollmann, Markus Kretsch, Rachael C Kurciński, Mateusz Li, Jun Li, Shuang Magnus, Marcin Masquida, BenoÎt Moafinejad, S Naeim Mondal, Arup Mukherjee, Sunandan Nguyen, Thi Hoang Duong Nikolaev, Grigory Nithin, Chandran Nye, Grace Pandaranadar Jeyeram, Iswarya P N Perez, Alberto Pham, Phillip Piccirilli, Joseph A Pilla, Smita Priyadarshini Pluta, Radosław Poblete, Simón Ponce-Salvatierra, Almudena Popenda, Mariusz Popenda, Lukasz Pucci, Fabrizio Rangan, Ramya Ray, Angana Ren, Aiming Sarzynska, Joanna Sha, Congzhou Mike Stefaniak, Filip Su, Zhaoming Suddala, Krishna C Szachniuk, Marta Townshend, Raphael Trachman, Robert J Wang, Jian Wang, Wenkai Watkins, Andrew Wirecki, Tomasz K Xiao, Yi Xiong, Peng Xiong, Yiduo Yang, Jianyi Yesselman, Joseph David Zhang, Jinwei Zhang, Yi Zhang, Zhenzhen Zhou, Yuanzhe Zok, Tomasz Zhang, Dong Zhang, Sicheng Żyła, Adriana Westhof, Eric Miao, Zhichao RNA Nucleic Acid Conformation Models, Molecular Computational Biology RNA, Catalytic Aptamers, Nucleotide RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson-Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest.
format	Artículo científico
id	pubmed_39623050
institution	PubMed
language	en
publishDate	2025
publisher	Nature methods
record_format	pubmed
spellingShingle	RNA-Puzzles Round V: blind predictions of 23 RNA structures. Bu, Fan Adam, Yagoub Adamiak, Ryszard W Antczak, Maciej de Aquino, Belisa Rebeca H Badepally, Nagendar Goud Batey, Robert T Baulin, Eugene F Boinski, Pawel Boniecki, Michal J Bujnicki, Janusz M Carpenter, Kristy A Chacon, Jose Chen, Shi-Jie Chiu, Wah Cordero, Pablo Das, Naba Krishna Das, Rhiju Dawson, Wayne K DiMaio, Frank Ding, Feng Dock-Bregeon, Anne-Catherine Dokholyan, Nikolay V Dror, Ron O Dunin-Horkawicz, Stanisław Eismann, Stephan Ennifar, Eric Esmaeeli, Reza Farsani, Masoud Amiri Ferré-D'Amaré, Adrian R Geniesse, Caleb Ghanim, George E Guzman, Horacio V Hood, Iris V Huang, Lin Jain, Dharm Skandh Jaryani, Farhang Jin, Lei Joshi, Astha Karelina, Masha Kieft, Jeffrey S Kladwang, Wipapat Kmiecik, Sebastian Koirala, Deepak Kollmann, Markus Kretsch, Rachael C Kurciński, Mateusz Li, Jun Li, Shuang Magnus, Marcin Masquida, BenoÎt Moafinejad, S Naeim Mondal, Arup Mukherjee, Sunandan Nguyen, Thi Hoang Duong Nikolaev, Grigory Nithin, Chandran Nye, Grace Pandaranadar Jeyeram, Iswarya P N Perez, Alberto Pham, Phillip Piccirilli, Joseph A Pilla, Smita Priyadarshini Pluta, Radosław Poblete, Simón Ponce-Salvatierra, Almudena Popenda, Mariusz Popenda, Lukasz Pucci, Fabrizio Rangan, Ramya Ray, Angana Ren, Aiming Sarzynska, Joanna Sha, Congzhou Mike Stefaniak, Filip Su, Zhaoming Suddala, Krishna C Szachniuk, Marta Townshend, Raphael Trachman, Robert J Wang, Jian Wang, Wenkai Watkins, Andrew Wirecki, Tomasz K Xiao, Yi Xiong, Peng Xiong, Yiduo Yang, Jianyi Yesselman, Joseph David Zhang, Jinwei Zhang, Yi Zhang, Zhenzhen Zhou, Yuanzhe Zok, Tomasz Zhang, Dong Zhang, Sicheng Żyła, Adriana Westhof, Eric Miao, Zhichao RNA Nucleic Acid Conformation Models, Molecular Computational Biology RNA, Catalytic Aptamers, Nucleotide RNA-Puzzles Round V: blind predictions of 23 RNA structures. Bu, Fan Adam, Yagoub Adamiak, Ryszard W Antczak, Maciej de Aquino, Belisa Rebeca H Badepally, Nagendar Goud Batey, Robert T Baulin, Eugene F Boinski, Pawel Boniecki, Michal J Bujnicki, Janusz M Carpenter, Kristy A Chacon, Jose Chen, Shi-Jie Chiu, Wah Cordero, Pablo Das, Naba Krishna Das, Rhiju Dawson, Wayne K DiMaio, Frank Ding, Feng Dock-Bregeon, Anne-Catherine Dokholyan, Nikolay V Dror, Ron O Dunin-Horkawicz, Stanisław Eismann, Stephan Ennifar, Eric Esmaeeli, Reza Farsani, Masoud Amiri Ferré-D'Amaré, Adrian R Geniesse, Caleb Ghanim, George E Guzman, Horacio V Hood, Iris V Huang, Lin Jain, Dharm Skandh Jaryani, Farhang Jin, Lei Joshi, Astha Karelina, Masha Kieft, Jeffrey S Kladwang, Wipapat Kmiecik, Sebastian Koirala, Deepak Kollmann, Markus Kretsch, Rachael C Kurciński, Mateusz Li, Jun Li, Shuang Magnus, Marcin Masquida, BenoÎt Moafinejad, S Naeim Mondal, Arup Mukherjee, Sunandan Nguyen, Thi Hoang Duong Nikolaev, Grigory Nithin, Chandran Nye, Grace Pandaranadar Jeyeram, Iswarya P N Perez, Alberto Pham, Phillip Piccirilli, Joseph A Pilla, Smita Priyadarshini Pluta, Radosław Poblete, Simón Ponce-Salvatierra, Almudena Popenda, Mariusz Popenda, Lukasz Pucci, Fabrizio Rangan, Ramya Ray, Angana Ren, Aiming Sarzynska, Joanna Sha, Congzhou Mike Stefaniak, Filip Su, Zhaoming Suddala, Krishna C Szachniuk, Marta Townshend, Raphael Trachman, Robert J Wang, Jian Wang, Wenkai Watkins, Andrew Wirecki, Tomasz K Xiao, Yi Xiong, Peng Xiong, Yiduo Yang, Jianyi Yesselman, Joseph David Zhang, Jinwei Zhang, Yi Zhang, Zhenzhen Zhou, Yuanzhe Zok, Tomasz Zhang, Dong Zhang, Sicheng Żyła, Adriana Westhof, Eric Miao, Zhichao RNA Nucleic Acid Conformation Models, Molecular Computational Biology RNA, Catalytic Aptamers, Nucleotide RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson-Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest.
title	RNA-Puzzles Round V: blind predictions of 23 RNA structures.
topic	RNA Nucleic Acid Conformation Models, Molecular Computational Biology RNA, Catalytic Aptamers, Nucleotide
url	https://pubmed.ncbi.nlm.nih.gov/39623050/