RNA-Puzzles Round V: blind predictions of 23 RNA structures
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 o...
Gespeichert in:
| Veröffentlicht in: | Nature methods 2024-12 |
|---|---|
| Hauptverfasser: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | |
|---|---|
| container_issue | |
| container_start_page | |
| container_title | Nature methods |
| container_volume | |
| creator | 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, 3rd, 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 |
| description | 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. |
| doi_str_mv | 10.1038/s41592-024-02543-9 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_osti_</sourceid><recordid>TN_cdi_osti_scitechconnect_2497760</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>3140922573</sourcerecordid><originalsourceid>FETCH-LOGICAL-c289t-b975a16377d64442c95def601070ba8263b274b85b3aa15f3f6f052c4f06d1183</originalsourceid><addsrcrecordid>eNo9kU9Lw0AQxRdRbK1-AQ8SPOkhOvsvm9VTKWqFolLU67LZbGgkzdbdRLCf3tS0PQzzGH7vHeYhdI7hBgNNbwPDXJIYCOuGMxrLAzTEnKWxwMAPdxokHqCTEL4AKGWEH6MBlQmhwGGI7ucv4_itXa8rG6K5a-s8-ryLsqrsxMrbvDRN6eoQuSIiNOrgKDS-NU3rbThFR4Wugj3b7hH6eHx4n0zj2evT82Q8iw1JZRNnUnCNEypEnjDGiJE8t0UCGARkOiUJzYhgWcozqjXmBS2SAjgxrIAkxzilI3TZ57rQlCqYsrFmYVxdW9MowqQQCXTQdQ8tdKVWvlxq_6ucLtV0PFObGzAJQkD6gzv2qmdX3n23NjRqWQZjq0rX1rVBUcxAEsIF7VDSo8a7ELwt9tkY1KYF1beguhbUfwtKdqaLbX6bLW2-t-zeTv8A1j595g</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>3140922573</pqid></control><display><type>article</type><title>RNA-Puzzles Round V: blind predictions of 23 RNA structures</title><source>SpringerLink Journals</source><source>Nature Journals Online</source><creator>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, 3rd, 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</creator><creatorcontrib>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, 3rd, 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 ; Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</creatorcontrib><description>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.</description><identifier>ISSN: 1548-7091</identifier><identifier>ISSN: 1548-7105</identifier><identifier>EISSN: 1548-7105</identifier><identifier>DOI: 10.1038/s41592-024-02543-9</identifier><identifier>PMID: 39623050</identifier><language>eng</language><publisher>United States: Nature Publishing Group</publisher><subject>Genetics ; Life Sciences ; software ; statistical methods</subject><ispartof>Nature methods, 2024-12</ispartof><rights>2024. The Author(s).</rights><rights>Distributed under a Creative Commons Attribution 4.0 International License</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c289t-b975a16377d64442c95def601070ba8263b274b85b3aa15f3f6f052c4f06d1183</cites><orcidid>0000-0001-5758-9416 ; 0000-0002-7524-8938 ; 0000-0001-7768-2802 ; 0000-0002-2114-173X ; 0000-0002-2121-365X ; 0000-0003-3966-8123 ; 0000-0003-1880-4536 ; 0000-0002-6172-5422 ; 0000-0003-4103-9238 ; 0000-0001-7751-7778 ; 0000-0002-0500-2238 ; 0000-0002-7011-1991 ; 0000-0002-5054-5338 ; 0000-0002-1676-860X ; 0000-0001-6874-2543 ; 0000-0003-4570-5170 ; 0000-0002-6418-2793 ; 0000-0002-7897-8338 ; 0000-0002-8225-4025 ; 0000-0001-6362-1451 ; 0000-0003-1117-3081 ; 0000-0001-8212-6093 ; 0000-0002-5320-2023 ; 0000-0003-4694-9783 ; 0000-0002-5769-5400 ; 0000-0003-2564-3005 ; 0000-0002-8724-7908 ; 0000-0002-5232-2234 ; 0000-0001-6424-3173 ; 0000-0002-0960-0825 ; 0000-0001-7497-0972 ; 0000-0003-4549-1619 ; 0000-0001-5301-9459 ; 0000-0001-8652-3651 ; 0000-0001-7623-0935 ; 0000-0003-2912-7737 ; 0000-0003-1597-2622 ; 0000-0002-0541-6270 ; 0000-0002-6633-165X ; 0000-0001-8374-6681 ; 0000-0003-1850-6336 ; 0000-0002-5420-4899 ; 0000-0003-4914-8228 ; 0000-0002-6935-518X ; 0000-0002-4361-0103 ; 0000-0002-5308-2746 ; 0000-0002-1384-6625 ; 0000-0003-0397-2596 ; 0000-0001-8603-8250 ; 0000-0002-4594-107X ; 0000-0002-5777-9815 ; 0000-0002-8910-3078 ; 0000-0002-6565-2099 ; 0000000303972596 ; 000000022114173X ; 0000000177517778 ; 0000000176230935 ; 0000000186038250 ; 0000000253202023 ; 000000021676860X ; 0000000287247908 ; 0000000205416270 ; 0000000253082746 ; 000000022121365X ; 0000000278978338 ; 0000000346949783 ; 0000000254204899 ; 0000000182126093 ; 0000000157589416 ; 0000000329127737 ; 0000000345705170 ; 0000000177682802 ; 0000000289103078 ; 0000000282254025 ; 000000026633165X ; 0000000349148228 ; 0000000275248938 ; 0000000183746681 ; 000000024594107X ; 0000000315972622 ; 0000000163621451 ; 0000000243610103 ; 0000000250545338 ; 0000000311173081 ; 0000000209600825 ; 0000000174970972 ; 0000000213846625 ; 0000000264182793 ; 0000000345491619 ; 0000000257695400 ; 0000000261725422 ; 000000026935518X ; 0000000318506336 ; 0000000339668123 ; 0000000257779815 ; 0000000168742543 ; 0000000325643005 ; 0000000318804536 ; 0000000270111991 ; 0000000341039238 ; 0000000164243173 ; 0000000186523651 ; 0000000252322234 ; 0000000153019459 ; 0000000205002238</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,776,780,881,27901,27902</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/39623050$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://hal.science/hal-04907708$$DView record in HAL$$Hfree_for_read</backlink><backlink>$$Uhttps://www.osti.gov/servlets/purl/2497760$$D View this record in Osti.gov$$Hfree_for_read</backlink></links><search><creatorcontrib>Bu, Fan</creatorcontrib><creatorcontrib>Adam, Yagoub</creatorcontrib><creatorcontrib>Adamiak, Ryszard W</creatorcontrib><creatorcontrib>Antczak, Maciej</creatorcontrib><creatorcontrib>de Aquino, Belisa Rebeca H</creatorcontrib><creatorcontrib>Badepally, Nagendar Goud</creatorcontrib><creatorcontrib>Batey, Robert T</creatorcontrib><creatorcontrib>Baulin, Eugene F</creatorcontrib><creatorcontrib>Boinski, Pawel</creatorcontrib><creatorcontrib>Boniecki, Michal J</creatorcontrib><creatorcontrib>Bujnicki, Janusz M</creatorcontrib><creatorcontrib>Carpenter, Kristy A</creatorcontrib><creatorcontrib>Chacon, Jose</creatorcontrib><creatorcontrib>Chen, Shi-Jie</creatorcontrib><creatorcontrib>Chiu, Wah</creatorcontrib><creatorcontrib>Cordero, Pablo</creatorcontrib><creatorcontrib>Das, Naba Krishna</creatorcontrib><creatorcontrib>Das, Rhiju</creatorcontrib><creatorcontrib>Dawson, Wayne K</creatorcontrib><creatorcontrib>DiMaio, Frank</creatorcontrib><creatorcontrib>Ding, Feng</creatorcontrib><creatorcontrib>Dock-Bregeon, Anne-Catherine</creatorcontrib><creatorcontrib>Dokholyan, Nikolay V</creatorcontrib><creatorcontrib>Dror, Ron O</creatorcontrib><creatorcontrib>Dunin-Horkawicz, Stanisław</creatorcontrib><creatorcontrib>Eismann, Stephan</creatorcontrib><creatorcontrib>Ennifar, Eric</creatorcontrib><creatorcontrib>Esmaeeli, Reza</creatorcontrib><creatorcontrib>Farsani, Masoud Amiri</creatorcontrib><creatorcontrib>Ferré-D'Amaré, Adrian R</creatorcontrib><creatorcontrib>Geniesse, Caleb</creatorcontrib><creatorcontrib>Ghanim, George E</creatorcontrib><creatorcontrib>Guzman, Horacio V</creatorcontrib><creatorcontrib>Hood, Iris V</creatorcontrib><creatorcontrib>Huang, Lin</creatorcontrib><creatorcontrib>Jain, Dharm Skandh</creatorcontrib><creatorcontrib>Jaryani, Farhang</creatorcontrib><creatorcontrib>Jin, Lei</creatorcontrib><creatorcontrib>Joshi, Astha</creatorcontrib><creatorcontrib>Karelina, Masha</creatorcontrib><creatorcontrib>Kieft, Jeffrey S</creatorcontrib><creatorcontrib>Kladwang, Wipapat</creatorcontrib><creatorcontrib>Kmiecik, Sebastian</creatorcontrib><creatorcontrib>Koirala, Deepak</creatorcontrib><creatorcontrib>Kollmann, Markus</creatorcontrib><creatorcontrib>Kretsch, Rachael C</creatorcontrib><creatorcontrib>Kurciński, Mateusz</creatorcontrib><creatorcontrib>Li, Jun</creatorcontrib><creatorcontrib>Li, Shuang</creatorcontrib><creatorcontrib>Magnus, Marcin</creatorcontrib><creatorcontrib>Masquida, BenoÎt</creatorcontrib><creatorcontrib>Moafinejad, S Naeim</creatorcontrib><creatorcontrib>Mondal, Arup</creatorcontrib><creatorcontrib>Mukherjee, Sunandan</creatorcontrib><creatorcontrib>Nguyen, Thi Hoang Duong</creatorcontrib><creatorcontrib>Nikolaev, Grigory</creatorcontrib><creatorcontrib>Nithin, Chandran</creatorcontrib><creatorcontrib>Nye, Grace</creatorcontrib><creatorcontrib>Pandaranadar Jeyeram, Iswarya P N</creatorcontrib><creatorcontrib>Perez, Alberto</creatorcontrib><creatorcontrib>Pham, Phillip</creatorcontrib><creatorcontrib>Piccirilli, Joseph A</creatorcontrib><creatorcontrib>Pilla, Smita Priyadarshini</creatorcontrib><creatorcontrib>Pluta, Radosław</creatorcontrib><creatorcontrib>Poblete, Simón</creatorcontrib><creatorcontrib>Ponce-Salvatierra, Almudena</creatorcontrib><creatorcontrib>Popenda, Mariusz</creatorcontrib><creatorcontrib>Popenda, Lukasz</creatorcontrib><creatorcontrib>Pucci, Fabrizio</creatorcontrib><creatorcontrib>Rangan, Ramya</creatorcontrib><creatorcontrib>Ray, Angana</creatorcontrib><creatorcontrib>Ren, Aiming</creatorcontrib><creatorcontrib>Sarzynska, Joanna</creatorcontrib><creatorcontrib>Sha, Congzhou Mike</creatorcontrib><creatorcontrib>Stefaniak, Filip</creatorcontrib><creatorcontrib>Su, Zhaoming</creatorcontrib><creatorcontrib>Suddala, Krishna C</creatorcontrib><creatorcontrib>Szachniuk, Marta</creatorcontrib><creatorcontrib>Townshend, Raphael</creatorcontrib><creatorcontrib>Trachman, 3rd, Robert J</creatorcontrib><creatorcontrib>Wang, Jian</creatorcontrib><creatorcontrib>Wang, Wenkai</creatorcontrib><creatorcontrib>Watkins, Andrew</creatorcontrib><creatorcontrib>Wirecki, Tomasz K</creatorcontrib><creatorcontrib>Xiao, Yi</creatorcontrib><creatorcontrib>Xiong, Peng</creatorcontrib><creatorcontrib>Xiong, Yiduo</creatorcontrib><creatorcontrib>Yang, Jianyi</creatorcontrib><creatorcontrib>Yesselman, Joseph David</creatorcontrib><creatorcontrib>Zhang, Jinwei</creatorcontrib><creatorcontrib>Zhang, Yi</creatorcontrib><creatorcontrib>Zhang, Zhenzhen</creatorcontrib><creatorcontrib>Zhou, Yuanzhe</creatorcontrib><creatorcontrib>Zok, Tomasz</creatorcontrib><creatorcontrib>Zhang, Dong</creatorcontrib><creatorcontrib>Zhang, Sicheng</creatorcontrib><creatorcontrib>Żyła, Adriana</creatorcontrib><creatorcontrib>Westhof, Eric</creatorcontrib><creatorcontrib>Miao, Zhichao</creatorcontrib><creatorcontrib>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</creatorcontrib><title>RNA-Puzzles Round V: blind predictions of 23 RNA structures</title><title>Nature methods</title><addtitle>Nat Methods</addtitle><description>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.</description><subject>Genetics</subject><subject>Life Sciences</subject><subject>software</subject><subject>statistical methods</subject><issn>1548-7091</issn><issn>1548-7105</issn><issn>1548-7105</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><recordid>eNo9kU9Lw0AQxRdRbK1-AQ8SPOkhOvsvm9VTKWqFolLU67LZbGgkzdbdRLCf3tS0PQzzGH7vHeYhdI7hBgNNbwPDXJIYCOuGMxrLAzTEnKWxwMAPdxokHqCTEL4AKGWEH6MBlQmhwGGI7ucv4_itXa8rG6K5a-s8-ryLsqrsxMrbvDRN6eoQuSIiNOrgKDS-NU3rbThFR4Wugj3b7hH6eHx4n0zj2evT82Q8iw1JZRNnUnCNEypEnjDGiJE8t0UCGARkOiUJzYhgWcozqjXmBS2SAjgxrIAkxzilI3TZ57rQlCqYsrFmYVxdW9MowqQQCXTQdQ8tdKVWvlxq_6ucLtV0PFObGzAJQkD6gzv2qmdX3n23NjRqWQZjq0rX1rVBUcxAEsIF7VDSo8a7ELwt9tkY1KYF1beguhbUfwtKdqaLbX6bLW2-t-zeTv8A1j595g</recordid><startdate>20241202</startdate><enddate>20241202</enddate><creator>Bu, Fan</creator><creator>Adam, Yagoub</creator><creator>Adamiak, Ryszard W</creator><creator>Antczak, Maciej</creator><creator>de Aquino, Belisa Rebeca H</creator><creator>Badepally, Nagendar Goud</creator><creator>Batey, Robert T</creator><creator>Baulin, Eugene F</creator><creator>Boinski, Pawel</creator><creator>Boniecki, Michal J</creator><creator>Bujnicki, Janusz M</creator><creator>Carpenter, Kristy A</creator><creator>Chacon, Jose</creator><creator>Chen, Shi-Jie</creator><creator>Chiu, Wah</creator><creator>Cordero, Pablo</creator><creator>Das, Naba Krishna</creator><creator>Das, Rhiju</creator><creator>Dawson, Wayne K</creator><creator>DiMaio, Frank</creator><creator>Ding, Feng</creator><creator>Dock-Bregeon, Anne-Catherine</creator><creator>Dokholyan, Nikolay V</creator><creator>Dror, Ron O</creator><creator>Dunin-Horkawicz, Stanisław</creator><creator>Eismann, Stephan</creator><creator>Ennifar, Eric</creator><creator>Esmaeeli, Reza</creator><creator>Farsani, Masoud Amiri</creator><creator>Ferré-D'Amaré, Adrian R</creator><creator>Geniesse, Caleb</creator><creator>Ghanim, George E</creator><creator>Guzman, Horacio V</creator><creator>Hood, Iris V</creator><creator>Huang, Lin</creator><creator>Jain, Dharm Skandh</creator><creator>Jaryani, Farhang</creator><creator>Jin, Lei</creator><creator>Joshi, Astha</creator><creator>Karelina, Masha</creator><creator>Kieft, Jeffrey S</creator><creator>Kladwang, Wipapat</creator><creator>Kmiecik, Sebastian</creator><creator>Koirala, Deepak</creator><creator>Kollmann, Markus</creator><creator>Kretsch, Rachael C</creator><creator>Kurciński, Mateusz</creator><creator>Li, Jun</creator><creator>Li, Shuang</creator><creator>Magnus, Marcin</creator><creator>Masquida, BenoÎt</creator><creator>Moafinejad, S Naeim</creator><creator>Mondal, Arup</creator><creator>Mukherjee, Sunandan</creator><creator>Nguyen, Thi Hoang Duong</creator><creator>Nikolaev, Grigory</creator><creator>Nithin, Chandran</creator><creator>Nye, Grace</creator><creator>Pandaranadar Jeyeram, Iswarya P N</creator><creator>Perez, Alberto</creator><creator>Pham, Phillip</creator><creator>Piccirilli, Joseph A</creator><creator>Pilla, Smita Priyadarshini</creator><creator>Pluta, Radosław</creator><creator>Poblete, Simón</creator><creator>Ponce-Salvatierra, Almudena</creator><creator>Popenda, Mariusz</creator><creator>Popenda, Lukasz</creator><creator>Pucci, Fabrizio</creator><creator>Rangan, Ramya</creator><creator>Ray, Angana</creator><creator>Ren, Aiming</creator><creator>Sarzynska, Joanna</creator><creator>Sha, Congzhou Mike</creator><creator>Stefaniak, Filip</creator><creator>Su, Zhaoming</creator><creator>Suddala, Krishna C</creator><creator>Szachniuk, Marta</creator><creator>Townshend, Raphael</creator><creator>Trachman, 3rd, Robert J</creator><creator>Wang, Jian</creator><creator>Wang, Wenkai</creator><creator>Watkins, Andrew</creator><creator>Wirecki, Tomasz K</creator><creator>Xiao, Yi</creator><creator>Xiong, Peng</creator><creator>Xiong, Yiduo</creator><creator>Yang, Jianyi</creator><creator>Yesselman, Joseph David</creator><creator>Zhang, Jinwei</creator><creator>Zhang, Yi</creator><creator>Zhang, Zhenzhen</creator><creator>Zhou, Yuanzhe</creator><creator>Zok, Tomasz</creator><creator>Zhang, Dong</creator><creator>Zhang, Sicheng</creator><creator>Żyła, Adriana</creator><creator>Westhof, Eric</creator><creator>Miao, Zhichao</creator><general>Nature Publishing Group</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>1XC</scope><scope>VOOES</scope><scope>OIOZB</scope><scope>OTOTI</scope><orcidid>https://orcid.org/0000-0001-5758-9416</orcidid><orcidid>https://orcid.org/0000-0002-7524-8938</orcidid><orcidid>https://orcid.org/0000-0001-7768-2802</orcidid><orcidid>https://orcid.org/0000-0002-2114-173X</orcidid><orcidid>https://orcid.org/0000-0002-2121-365X</orcidid><orcidid>https://orcid.org/0000-0003-3966-8123</orcidid><orcidid>https://orcid.org/0000-0003-1880-4536</orcidid><orcidid>https://orcid.org/0000-0002-6172-5422</orcidid><orcidid>https://orcid.org/0000-0003-4103-9238</orcidid><orcidid>https://orcid.org/0000-0001-7751-7778</orcidid><orcidid>https://orcid.org/0000-0002-0500-2238</orcidid><orcidid>https://orcid.org/0000-0002-7011-1991</orcidid><orcidid>https://orcid.org/0000-0002-5054-5338</orcidid><orcidid>https://orcid.org/0000-0002-1676-860X</orcidid><orcidid>https://orcid.org/0000-0001-6874-2543</orcidid><orcidid>https://orcid.org/0000-0003-4570-5170</orcidid><orcidid>https://orcid.org/0000-0002-6418-2793</orcidid><orcidid>https://orcid.org/0000-0002-7897-8338</orcidid><orcidid>https://orcid.org/0000-0002-8225-4025</orcidid><orcidid>https://orcid.org/0000-0001-6362-1451</orcidid><orcidid>https://orcid.org/0000-0003-1117-3081</orcidid><orcidid>https://orcid.org/0000-0001-8212-6093</orcidid><orcidid>https://orcid.org/0000-0002-5320-2023</orcidid><orcidid>https://orcid.org/0000-0003-4694-9783</orcidid><orcidid>https://orcid.org/0000-0002-5769-5400</orcidid><orcidid>https://orcid.org/0000-0003-2564-3005</orcidid><orcidid>https://orcid.org/0000-0002-8724-7908</orcidid><orcidid>https://orcid.org/0000-0002-5232-2234</orcidid><orcidid>https://orcid.org/0000-0001-6424-3173</orcidid><orcidid>https://orcid.org/0000-0002-0960-0825</orcidid><orcidid>https://orcid.org/0000-0001-7497-0972</orcidid><orcidid>https://orcid.org/0000-0003-4549-1619</orcidid><orcidid>https://orcid.org/0000-0001-5301-9459</orcidid><orcidid>https://orcid.org/0000-0001-8652-3651</orcidid><orcidid>https://orcid.org/0000-0001-7623-0935</orcidid><orcidid>https://orcid.org/0000-0003-2912-7737</orcidid><orcidid>https://orcid.org/0000-0003-1597-2622</orcidid><orcidid>https://orcid.org/0000-0002-0541-6270</orcidid><orcidid>https://orcid.org/0000-0002-6633-165X</orcidid><orcidid>https://orcid.org/0000-0001-8374-6681</orcidid><orcidid>https://orcid.org/0000-0003-1850-6336</orcidid><orcidid>https://orcid.org/0000-0002-5420-4899</orcidid><orcidid>https://orcid.org/0000-0003-4914-8228</orcidid><orcidid>https://orcid.org/0000-0002-6935-518X</orcidid><orcidid>https://orcid.org/0000-0002-4361-0103</orcidid><orcidid>https://orcid.org/0000-0002-5308-2746</orcidid><orcidid>https://orcid.org/0000-0002-1384-6625</orcidid><orcidid>https://orcid.org/0000-0003-0397-2596</orcidid><orcidid>https://orcid.org/0000-0001-8603-8250</orcidid><orcidid>https://orcid.org/0000-0002-4594-107X</orcidid><orcidid>https://orcid.org/0000-0002-5777-9815</orcidid><orcidid>https://orcid.org/0000-0002-8910-3078</orcidid><orcidid>https://orcid.org/0000-0002-6565-2099</orcidid><orcidid>https://orcid.org/0000000303972596</orcidid><orcidid>https://orcid.org/000000022114173X</orcidid><orcidid>https://orcid.org/0000000177517778</orcidid><orcidid>https://orcid.org/0000000176230935</orcidid><orcidid>https://orcid.org/0000000186038250</orcidid><orcidid>https://orcid.org/0000000253202023</orcidid><orcidid>https://orcid.org/000000021676860X</orcidid><orcidid>https://orcid.org/0000000287247908</orcidid><orcidid>https://orcid.org/0000000205416270</orcidid><orcidid>https://orcid.org/0000000253082746</orcidid><orcidid>https://orcid.org/000000022121365X</orcidid><orcidid>https://orcid.org/0000000278978338</orcidid><orcidid>https://orcid.org/0000000346949783</orcidid><orcidid>https://orcid.org/0000000254204899</orcidid><orcidid>https://orcid.org/0000000182126093</orcidid><orcidid>https://orcid.org/0000000157589416</orcidid><orcidid>https://orcid.org/0000000329127737</orcidid><orcidid>https://orcid.org/0000000345705170</orcidid><orcidid>https://orcid.org/0000000177682802</orcidid><orcidid>https://orcid.org/0000000289103078</orcidid><orcidid>https://orcid.org/0000000282254025</orcidid><orcidid>https://orcid.org/000000026633165X</orcidid><orcidid>https://orcid.org/0000000349148228</orcidid><orcidid>https://orcid.org/0000000275248938</orcidid><orcidid>https://orcid.org/0000000183746681</orcidid><orcidid>https://orcid.org/000000024594107X</orcidid><orcidid>https://orcid.org/0000000315972622</orcidid><orcidid>https://orcid.org/0000000163621451</orcidid><orcidid>https://orcid.org/0000000243610103</orcidid><orcidid>https://orcid.org/0000000250545338</orcidid><orcidid>https://orcid.org/0000000311173081</orcidid><orcidid>https://orcid.org/0000000209600825</orcidid><orcidid>https://orcid.org/0000000174970972</orcidid><orcidid>https://orcid.org/0000000213846625</orcidid><orcidid>https://orcid.org/0000000264182793</orcidid><orcidid>https://orcid.org/0000000345491619</orcidid><orcidid>https://orcid.org/0000000257695400</orcidid><orcidid>https://orcid.org/0000000261725422</orcidid><orcidid>https://orcid.org/000000026935518X</orcidid><orcidid>https://orcid.org/0000000318506336</orcidid><orcidid>https://orcid.org/0000000339668123</orcidid><orcidid>https://orcid.org/0000000257779815</orcidid><orcidid>https://orcid.org/0000000168742543</orcidid><orcidid>https://orcid.org/0000000325643005</orcidid><orcidid>https://orcid.org/0000000318804536</orcidid><orcidid>https://orcid.org/0000000270111991</orcidid><orcidid>https://orcid.org/0000000341039238</orcidid><orcidid>https://orcid.org/0000000164243173</orcidid><orcidid>https://orcid.org/0000000186523651</orcidid><orcidid>https://orcid.org/0000000252322234</orcidid><orcidid>https://orcid.org/0000000153019459</orcidid><orcidid>https://orcid.org/0000000205002238</orcidid></search><sort><creationdate>20241202</creationdate><title>RNA-Puzzles Round V: blind predictions of 23 RNA structures</title><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, 3rd, 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></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c289t-b975a16377d64442c95def601070ba8263b274b85b3aa15f3f6f052c4f06d1183</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Genetics</topic><topic>Life Sciences</topic><topic>software</topic><topic>statistical methods</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Bu, Fan</creatorcontrib><creatorcontrib>Adam, Yagoub</creatorcontrib><creatorcontrib>Adamiak, Ryszard W</creatorcontrib><creatorcontrib>Antczak, Maciej</creatorcontrib><creatorcontrib>de Aquino, Belisa Rebeca H</creatorcontrib><creatorcontrib>Badepally, Nagendar Goud</creatorcontrib><creatorcontrib>Batey, Robert T</creatorcontrib><creatorcontrib>Baulin, Eugene F</creatorcontrib><creatorcontrib>Boinski, Pawel</creatorcontrib><creatorcontrib>Boniecki, Michal J</creatorcontrib><creatorcontrib>Bujnicki, Janusz M</creatorcontrib><creatorcontrib>Carpenter, Kristy A</creatorcontrib><creatorcontrib>Chacon, Jose</creatorcontrib><creatorcontrib>Chen, Shi-Jie</creatorcontrib><creatorcontrib>Chiu, Wah</creatorcontrib><creatorcontrib>Cordero, Pablo</creatorcontrib><creatorcontrib>Das, Naba Krishna</creatorcontrib><creatorcontrib>Das, Rhiju</creatorcontrib><creatorcontrib>Dawson, Wayne K</creatorcontrib><creatorcontrib>DiMaio, Frank</creatorcontrib><creatorcontrib>Ding, Feng</creatorcontrib><creatorcontrib>Dock-Bregeon, Anne-Catherine</creatorcontrib><creatorcontrib>Dokholyan, Nikolay V</creatorcontrib><creatorcontrib>Dror, Ron O</creatorcontrib><creatorcontrib>Dunin-Horkawicz, Stanisław</creatorcontrib><creatorcontrib>Eismann, Stephan</creatorcontrib><creatorcontrib>Ennifar, Eric</creatorcontrib><creatorcontrib>Esmaeeli, Reza</creatorcontrib><creatorcontrib>Farsani, Masoud Amiri</creatorcontrib><creatorcontrib>Ferré-D'Amaré, Adrian R</creatorcontrib><creatorcontrib>Geniesse, Caleb</creatorcontrib><creatorcontrib>Ghanim, George E</creatorcontrib><creatorcontrib>Guzman, Horacio V</creatorcontrib><creatorcontrib>Hood, Iris V</creatorcontrib><creatorcontrib>Huang, Lin</creatorcontrib><creatorcontrib>Jain, Dharm Skandh</creatorcontrib><creatorcontrib>Jaryani, Farhang</creatorcontrib><creatorcontrib>Jin, Lei</creatorcontrib><creatorcontrib>Joshi, Astha</creatorcontrib><creatorcontrib>Karelina, Masha</creatorcontrib><creatorcontrib>Kieft, Jeffrey S</creatorcontrib><creatorcontrib>Kladwang, Wipapat</creatorcontrib><creatorcontrib>Kmiecik, Sebastian</creatorcontrib><creatorcontrib>Koirala, Deepak</creatorcontrib><creatorcontrib>Kollmann, Markus</creatorcontrib><creatorcontrib>Kretsch, Rachael C</creatorcontrib><creatorcontrib>Kurciński, Mateusz</creatorcontrib><creatorcontrib>Li, Jun</creatorcontrib><creatorcontrib>Li, Shuang</creatorcontrib><creatorcontrib>Magnus, Marcin</creatorcontrib><creatorcontrib>Masquida, BenoÎt</creatorcontrib><creatorcontrib>Moafinejad, S Naeim</creatorcontrib><creatorcontrib>Mondal, Arup</creatorcontrib><creatorcontrib>Mukherjee, Sunandan</creatorcontrib><creatorcontrib>Nguyen, Thi Hoang Duong</creatorcontrib><creatorcontrib>Nikolaev, Grigory</creatorcontrib><creatorcontrib>Nithin, Chandran</creatorcontrib><creatorcontrib>Nye, Grace</creatorcontrib><creatorcontrib>Pandaranadar Jeyeram, Iswarya P N</creatorcontrib><creatorcontrib>Perez, Alberto</creatorcontrib><creatorcontrib>Pham, Phillip</creatorcontrib><creatorcontrib>Piccirilli, Joseph A</creatorcontrib><creatorcontrib>Pilla, Smita Priyadarshini</creatorcontrib><creatorcontrib>Pluta, Radosław</creatorcontrib><creatorcontrib>Poblete, Simón</creatorcontrib><creatorcontrib>Ponce-Salvatierra, Almudena</creatorcontrib><creatorcontrib>Popenda, Mariusz</creatorcontrib><creatorcontrib>Popenda, Lukasz</creatorcontrib><creatorcontrib>Pucci, Fabrizio</creatorcontrib><creatorcontrib>Rangan, Ramya</creatorcontrib><creatorcontrib>Ray, Angana</creatorcontrib><creatorcontrib>Ren, Aiming</creatorcontrib><creatorcontrib>Sarzynska, Joanna</creatorcontrib><creatorcontrib>Sha, Congzhou Mike</creatorcontrib><creatorcontrib>Stefaniak, Filip</creatorcontrib><creatorcontrib>Su, Zhaoming</creatorcontrib><creatorcontrib>Suddala, Krishna C</creatorcontrib><creatorcontrib>Szachniuk, Marta</creatorcontrib><creatorcontrib>Townshend, Raphael</creatorcontrib><creatorcontrib>Trachman, 3rd, Robert J</creatorcontrib><creatorcontrib>Wang, Jian</creatorcontrib><creatorcontrib>Wang, Wenkai</creatorcontrib><creatorcontrib>Watkins, Andrew</creatorcontrib><creatorcontrib>Wirecki, Tomasz K</creatorcontrib><creatorcontrib>Xiao, Yi</creatorcontrib><creatorcontrib>Xiong, Peng</creatorcontrib><creatorcontrib>Xiong, Yiduo</creatorcontrib><creatorcontrib>Yang, Jianyi</creatorcontrib><creatorcontrib>Yesselman, Joseph David</creatorcontrib><creatorcontrib>Zhang, Jinwei</creatorcontrib><creatorcontrib>Zhang, Yi</creatorcontrib><creatorcontrib>Zhang, Zhenzhen</creatorcontrib><creatorcontrib>Zhou, Yuanzhe</creatorcontrib><creatorcontrib>Zok, Tomasz</creatorcontrib><creatorcontrib>Zhang, Dong</creatorcontrib><creatorcontrib>Zhang, Sicheng</creatorcontrib><creatorcontrib>Żyła, Adriana</creatorcontrib><creatorcontrib>Westhof, Eric</creatorcontrib><creatorcontrib>Miao, Zhichao</creatorcontrib><creatorcontrib>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>OSTI.GOV - Hybrid</collection><collection>OSTI.GOV</collection><jtitle>Nature methods</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Bu, Fan</au><au>Adam, Yagoub</au><au>Adamiak, Ryszard W</au><au>Antczak, Maciej</au><au>de Aquino, Belisa Rebeca H</au><au>Badepally, Nagendar Goud</au><au>Batey, Robert T</au><au>Baulin, Eugene F</au><au>Boinski, Pawel</au><au>Boniecki, Michal J</au><au>Bujnicki, Janusz M</au><au>Carpenter, Kristy A</au><au>Chacon, Jose</au><au>Chen, Shi-Jie</au><au>Chiu, Wah</au><au>Cordero, Pablo</au><au>Das, Naba Krishna</au><au>Das, Rhiju</au><au>Dawson, Wayne K</au><au>DiMaio, Frank</au><au>Ding, Feng</au><au>Dock-Bregeon, Anne-Catherine</au><au>Dokholyan, Nikolay V</au><au>Dror, Ron O</au><au>Dunin-Horkawicz, Stanisław</au><au>Eismann, Stephan</au><au>Ennifar, Eric</au><au>Esmaeeli, Reza</au><au>Farsani, Masoud Amiri</au><au>Ferré-D'Amaré, Adrian R</au><au>Geniesse, Caleb</au><au>Ghanim, George E</au><au>Guzman, Horacio V</au><au>Hood, Iris V</au><au>Huang, Lin</au><au>Jain, Dharm Skandh</au><au>Jaryani, Farhang</au><au>Jin, Lei</au><au>Joshi, Astha</au><au>Karelina, Masha</au><au>Kieft, Jeffrey S</au><au>Kladwang, Wipapat</au><au>Kmiecik, Sebastian</au><au>Koirala, Deepak</au><au>Kollmann, Markus</au><au>Kretsch, Rachael C</au><au>Kurciński, Mateusz</au><au>Li, Jun</au><au>Li, Shuang</au><au>Magnus, Marcin</au><au>Masquida, BenoÎt</au><au>Moafinejad, S Naeim</au><au>Mondal, Arup</au><au>Mukherjee, Sunandan</au><au>Nguyen, Thi Hoang Duong</au><au>Nikolaev, Grigory</au><au>Nithin, Chandran</au><au>Nye, Grace</au><au>Pandaranadar Jeyeram, Iswarya P N</au><au>Perez, Alberto</au><au>Pham, Phillip</au><au>Piccirilli, Joseph A</au><au>Pilla, Smita Priyadarshini</au><au>Pluta, Radosław</au><au>Poblete, Simón</au><au>Ponce-Salvatierra, Almudena</au><au>Popenda, Mariusz</au><au>Popenda, Lukasz</au><au>Pucci, Fabrizio</au><au>Rangan, Ramya</au><au>Ray, Angana</au><au>Ren, Aiming</au><au>Sarzynska, Joanna</au><au>Sha, Congzhou Mike</au><au>Stefaniak, Filip</au><au>Su, Zhaoming</au><au>Suddala, Krishna C</au><au>Szachniuk, Marta</au><au>Townshend, Raphael</au><au>Trachman, 3rd, Robert J</au><au>Wang, Jian</au><au>Wang, Wenkai</au><au>Watkins, Andrew</au><au>Wirecki, Tomasz K</au><au>Xiao, Yi</au><au>Xiong, Peng</au><au>Xiong, Yiduo</au><au>Yang, Jianyi</au><au>Yesselman, Joseph David</au><au>Zhang, Jinwei</au><au>Zhang, Yi</au><au>Zhang, Zhenzhen</au><au>Zhou, Yuanzhe</au><au>Zok, Tomasz</au><au>Zhang, Dong</au><au>Zhang, Sicheng</au><au>Żyła, Adriana</au><au>Westhof, Eric</au><au>Miao, Zhichao</au><aucorp>Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>RNA-Puzzles Round V: blind predictions of 23 RNA structures</atitle><jtitle>Nature methods</jtitle><addtitle>Nat Methods</addtitle><date>2024-12-02</date><risdate>2024</risdate><issn>1548-7091</issn><issn>1548-7105</issn><eissn>1548-7105</eissn><abstract>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.</abstract><cop>United States</cop><pub>Nature Publishing Group</pub><pmid>39623050</pmid><doi>10.1038/s41592-024-02543-9</doi><orcidid>https://orcid.org/0000-0001-5758-9416</orcidid><orcidid>https://orcid.org/0000-0002-7524-8938</orcidid><orcidid>https://orcid.org/0000-0001-7768-2802</orcidid><orcidid>https://orcid.org/0000-0002-2114-173X</orcidid><orcidid>https://orcid.org/0000-0002-2121-365X</orcidid><orcidid>https://orcid.org/0000-0003-3966-8123</orcidid><orcidid>https://orcid.org/0000-0003-1880-4536</orcidid><orcidid>https://orcid.org/0000-0002-6172-5422</orcidid><orcidid>https://orcid.org/0000-0003-4103-9238</orcidid><orcidid>https://orcid.org/0000-0001-7751-7778</orcidid><orcidid>https://orcid.org/0000-0002-0500-2238</orcidid><orcidid>https://orcid.org/0000-0002-7011-1991</orcidid><orcidid>https://orcid.org/0000-0002-5054-5338</orcidid><orcidid>https://orcid.org/0000-0002-1676-860X</orcidid><orcidid>https://orcid.org/0000-0001-6874-2543</orcidid><orcidid>https://orcid.org/0000-0003-4570-5170</orcidid><orcidid>https://orcid.org/0000-0002-6418-2793</orcidid><orcidid>https://orcid.org/0000-0002-7897-8338</orcidid><orcidid>https://orcid.org/0000-0002-8225-4025</orcidid><orcidid>https://orcid.org/0000-0001-6362-1451</orcidid><orcidid>https://orcid.org/0000-0003-1117-3081</orcidid><orcidid>https://orcid.org/0000-0001-8212-6093</orcidid><orcidid>https://orcid.org/0000-0002-5320-2023</orcidid><orcidid>https://orcid.org/0000-0003-4694-9783</orcidid><orcidid>https://orcid.org/0000-0002-5769-5400</orcidid><orcidid>https://orcid.org/0000-0003-2564-3005</orcidid><orcidid>https://orcid.org/0000-0002-8724-7908</orcidid><orcidid>https://orcid.org/0000-0002-5232-2234</orcidid><orcidid>https://orcid.org/0000-0001-6424-3173</orcidid><orcidid>https://orcid.org/0000-0002-0960-0825</orcidid><orcidid>https://orcid.org/0000-0001-7497-0972</orcidid><orcidid>https://orcid.org/0000-0003-4549-1619</orcidid><orcidid>https://orcid.org/0000-0001-5301-9459</orcidid><orcidid>https://orcid.org/0000-0001-8652-3651</orcidid><orcidid>https://orcid.org/0000-0001-7623-0935</orcidid><orcidid>https://orcid.org/0000-0003-2912-7737</orcidid><orcidid>https://orcid.org/0000-0003-1597-2622</orcidid><orcidid>https://orcid.org/0000-0002-0541-6270</orcidid><orcidid>https://orcid.org/0000-0002-6633-165X</orcidid><orcidid>https://orcid.org/0000-0001-8374-6681</orcidid><orcidid>https://orcid.org/0000-0003-1850-6336</orcidid><orcidid>https://orcid.org/0000-0002-5420-4899</orcidid><orcidid>https://orcid.org/0000-0003-4914-8228</orcidid><orcidid>https://orcid.org/0000-0002-6935-518X</orcidid><orcidid>https://orcid.org/0000-0002-4361-0103</orcidid><orcidid>https://orcid.org/0000-0002-5308-2746</orcidid><orcidid>https://orcid.org/0000-0002-1384-6625</orcidid><orcidid>https://orcid.org/0000-0003-0397-2596</orcidid><orcidid>https://orcid.org/0000-0001-8603-8250</orcidid><orcidid>https://orcid.org/0000-0002-4594-107X</orcidid><orcidid>https://orcid.org/0000-0002-5777-9815</orcidid><orcidid>https://orcid.org/0000-0002-8910-3078</orcidid><orcidid>https://orcid.org/0000-0002-6565-2099</orcidid><orcidid>https://orcid.org/0000000303972596</orcidid><orcidid>https://orcid.org/000000022114173X</orcidid><orcidid>https://orcid.org/0000000177517778</orcidid><orcidid>https://orcid.org/0000000176230935</orcidid><orcidid>https://orcid.org/0000000186038250</orcidid><orcidid>https://orcid.org/0000000253202023</orcidid><orcidid>https://orcid.org/000000021676860X</orcidid><orcidid>https://orcid.org/0000000287247908</orcidid><orcidid>https://orcid.org/0000000205416270</orcidid><orcidid>https://orcid.org/0000000253082746</orcidid><orcidid>https://orcid.org/000000022121365X</orcidid><orcidid>https://orcid.org/0000000278978338</orcidid><orcidid>https://orcid.org/0000000346949783</orcidid><orcidid>https://orcid.org/0000000254204899</orcidid><orcidid>https://orcid.org/0000000182126093</orcidid><orcidid>https://orcid.org/0000000157589416</orcidid><orcidid>https://orcid.org/0000000329127737</orcidid><orcidid>https://orcid.org/0000000345705170</orcidid><orcidid>https://orcid.org/0000000177682802</orcidid><orcidid>https://orcid.org/0000000289103078</orcidid><orcidid>https://orcid.org/0000000282254025</orcidid><orcidid>https://orcid.org/000000026633165X</orcidid><orcidid>https://orcid.org/0000000349148228</orcidid><orcidid>https://orcid.org/0000000275248938</orcidid><orcidid>https://orcid.org/0000000183746681</orcidid><orcidid>https://orcid.org/000000024594107X</orcidid><orcidid>https://orcid.org/0000000315972622</orcidid><orcidid>https://orcid.org/0000000163621451</orcidid><orcidid>https://orcid.org/0000000243610103</orcidid><orcidid>https://orcid.org/0000000250545338</orcidid><orcidid>https://orcid.org/0000000311173081</orcidid><orcidid>https://orcid.org/0000000209600825</orcidid><orcidid>https://orcid.org/0000000174970972</orcidid><orcidid>https://orcid.org/0000000213846625</orcidid><orcidid>https://orcid.org/0000000264182793</orcidid><orcidid>https://orcid.org/0000000345491619</orcidid><orcidid>https://orcid.org/0000000257695400</orcidid><orcidid>https://orcid.org/0000000261725422</orcidid><orcidid>https://orcid.org/000000026935518X</orcidid><orcidid>https://orcid.org/0000000318506336</orcidid><orcidid>https://orcid.org/0000000339668123</orcidid><orcidid>https://orcid.org/0000000257779815</orcidid><orcidid>https://orcid.org/0000000168742543</orcidid><orcidid>https://orcid.org/0000000325643005</orcidid><orcidid>https://orcid.org/0000000318804536</orcidid><orcidid>https://orcid.org/0000000270111991</orcidid><orcidid>https://orcid.org/0000000341039238</orcidid><orcidid>https://orcid.org/0000000164243173</orcidid><orcidid>https://orcid.org/0000000186523651</orcidid><orcidid>https://orcid.org/0000000252322234</orcidid><orcidid>https://orcid.org/0000000153019459</orcidid><orcidid>https://orcid.org/0000000205002238</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1548-7091 |
| ispartof | Nature methods, 2024-12 |
| issn | 1548-7091 1548-7105 1548-7105 |
| language | eng |
| recordid | cdi_osti_scitechconnect_2497760 |
| source | SpringerLink Journals; Nature Journals Online |
| subjects | Genetics Life Sciences software statistical methods |
| title | RNA-Puzzles Round V: blind predictions of 23 RNA structures |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-09T08%3A27%3A31IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_osti_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=RNA-Puzzles%20Round%20V:%20blind%20predictions%20of%2023%20RNA%20structures&rft.jtitle=Nature%20methods&rft.au=Bu,%20Fan&rft.aucorp=Lawrence%20Berkeley%20National%20Laboratory%20(LBNL),%20Berkeley,%20CA%20(United%20States)&rft.date=2024-12-02&rft.issn=1548-7091&rft.eissn=1548-7105&rft_id=info:doi/10.1038/s41592-024-02543-9&rft_dat=%3Cproquest_osti_%3E3140922573%3C/proquest_osti_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=3140922573&rft_id=info:pmid/39623050&rfr_iscdi=true |