An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
Abstract Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require n...
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2018
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oai:doaj.org-article:b0b847aec1154062a3c86bac14d94e552021-12-02T15:08:25ZAn analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP1210.1038/s41598-018-26812-82045-2322https://doaj.org/article/b0b847aec1154062a3c86bac14d94e552018-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-26812-8https://doaj.org/toc/2045-2322Abstract Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research.Chen KeasarLiam J. McGuffinBjörn WallnerGaurav ChopraBadri AdhikariDebswapna BhattacharyaLauren BlakeLeandro Oliveira BortotRenzhi CaoB. K. DhanasekaranItzhel DimasRodrigo Antonio FaccioliEshel FaraggiRobert GanzynkowiczSambit GhoshSoma GhoshArtur GiełdońLukasz GolonYi HeLim HeoJie HouMain KhanFiras KhatibGeorge A. KhouryChris KieslichDavid E. KimPawel KrupaGyu Rie LeeHongbo LiJilong LiAgnieszka LipskaAdam LiwoAli Hassan A. MaghrabiMilot MirditaShokoufeh MirzaeiMagdalena A. MozolewskaMelis OnelSergey OvchinnikovAnand ShahUtkarsh ShahTomer SidiAdam K. SieradzanMagdalena ŚlusarzRafal ŚlusarzJames SmadbeckPhanourios TamamisNicholas TrieberTomasz WireckiYanping YinYang ZhangJaume BacarditMaciej BaranowskiNicholas ChapmanSeth CooperAlexandre DefelicibusJeff FlattenBrian KoepnickZoran PopovićBartlomiej ZaborowskiDavid BakerJianlin ChengCezary CzaplewskiAlexandre Cláudio Botazzo DelbemChristodoulos FloudasAndrzej KloczkowskiStanislaw OłdziejMichael LevittHarold ScheragaChaok SeokJohannes SödingSaraswathi VishveshwaraDong XuFoldit Players consortiumSilvia N. CrivelliNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-18 (2018) |
| institution |
DOAJ |
| collection |
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| language |
EN |
| topic |
Medicine R Science Q |
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Medicine R Science Q Chen Keasar Liam J. McGuffin Björn Wallner Gaurav Chopra Badri Adhikari Debswapna Bhattacharya Lauren Blake Leandro Oliveira Bortot Renzhi Cao B. K. Dhanasekaran Itzhel Dimas Rodrigo Antonio Faccioli Eshel Faraggi Robert Ganzynkowicz Sambit Ghosh Soma Ghosh Artur Giełdoń Lukasz Golon Yi He Lim Heo Jie Hou Main Khan Firas Khatib George A. Khoury Chris Kieslich David E. Kim Pawel Krupa Gyu Rie Lee Hongbo Li Jilong Li Agnieszka Lipska Adam Liwo Ali Hassan A. Maghrabi Milot Mirdita Shokoufeh Mirzaei Magdalena A. Mozolewska Melis Onel Sergey Ovchinnikov Anand Shah Utkarsh Shah Tomer Sidi Adam K. Sieradzan Magdalena Ślusarz Rafal Ślusarz James Smadbeck Phanourios Tamamis Nicholas Trieber Tomasz Wirecki Yanping Yin Yang Zhang Jaume Bacardit Maciej Baranowski Nicholas Chapman Seth Cooper Alexandre Defelicibus Jeff Flatten Brian Koepnick Zoran Popović Bartlomiej Zaborowski David Baker Jianlin Cheng Cezary Czaplewski Alexandre Cláudio Botazzo Delbem Christodoulos Floudas Andrzej Kloczkowski Stanislaw Ołdziej Michael Levitt Harold Scheraga Chaok Seok Johannes Söding Saraswathi Vishveshwara Dong Xu Foldit Players consortium Silvia N. Crivelli An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 |
| description |
Abstract Every two years groups worldwide participate in the Critical Assessment of Protein Structure Prediction (CASP) experiment to blindly test the strengths and weaknesses of their computational methods. CASP has significantly advanced the field but many hurdles still remain, which may require new ideas and collaborations. In 2012 a web-based effort called WeFold, was initiated to promote collaboration within the CASP community and attract researchers from other fields to contribute new ideas to CASP. Members of the WeFold coopetition (cooperation and competition) participated in CASP as individual teams, but also shared components of their methods to create hybrid pipelines and actively contributed to this effort. We assert that the scale and diversity of integrative prediction pipelines could not have been achieved by any individual lab or even by any collaboration among a few partners. The models contributed by the participating groups and generated by the pipelines are publicly available at the WeFold website providing a wealth of data that remains to be tapped. Here, we analyze the results of the 2014 and 2016 pipelines showing improvements according to the CASP assessment as well as areas that require further adjustments and research. |
| format |
article |
| author |
Chen Keasar Liam J. McGuffin Björn Wallner Gaurav Chopra Badri Adhikari Debswapna Bhattacharya Lauren Blake Leandro Oliveira Bortot Renzhi Cao B. K. Dhanasekaran Itzhel Dimas Rodrigo Antonio Faccioli Eshel Faraggi Robert Ganzynkowicz Sambit Ghosh Soma Ghosh Artur Giełdoń Lukasz Golon Yi He Lim Heo Jie Hou Main Khan Firas Khatib George A. Khoury Chris Kieslich David E. Kim Pawel Krupa Gyu Rie Lee Hongbo Li Jilong Li Agnieszka Lipska Adam Liwo Ali Hassan A. Maghrabi Milot Mirdita Shokoufeh Mirzaei Magdalena A. Mozolewska Melis Onel Sergey Ovchinnikov Anand Shah Utkarsh Shah Tomer Sidi Adam K. Sieradzan Magdalena Ślusarz Rafal Ślusarz James Smadbeck Phanourios Tamamis Nicholas Trieber Tomasz Wirecki Yanping Yin Yang Zhang Jaume Bacardit Maciej Baranowski Nicholas Chapman Seth Cooper Alexandre Defelicibus Jeff Flatten Brian Koepnick Zoran Popović Bartlomiej Zaborowski David Baker Jianlin Cheng Cezary Czaplewski Alexandre Cláudio Botazzo Delbem Christodoulos Floudas Andrzej Kloczkowski Stanislaw Ołdziej Michael Levitt Harold Scheraga Chaok Seok Johannes Söding Saraswathi Vishveshwara Dong Xu Foldit Players consortium Silvia N. Crivelli |
| author_facet |
Chen Keasar Liam J. McGuffin Björn Wallner Gaurav Chopra Badri Adhikari Debswapna Bhattacharya Lauren Blake Leandro Oliveira Bortot Renzhi Cao B. K. Dhanasekaran Itzhel Dimas Rodrigo Antonio Faccioli Eshel Faraggi Robert Ganzynkowicz Sambit Ghosh Soma Ghosh Artur Giełdoń Lukasz Golon Yi He Lim Heo Jie Hou Main Khan Firas Khatib George A. Khoury Chris Kieslich David E. Kim Pawel Krupa Gyu Rie Lee Hongbo Li Jilong Li Agnieszka Lipska Adam Liwo Ali Hassan A. Maghrabi Milot Mirdita Shokoufeh Mirzaei Magdalena A. Mozolewska Melis Onel Sergey Ovchinnikov Anand Shah Utkarsh Shah Tomer Sidi Adam K. Sieradzan Magdalena Ślusarz Rafal Ślusarz James Smadbeck Phanourios Tamamis Nicholas Trieber Tomasz Wirecki Yanping Yin Yang Zhang Jaume Bacardit Maciej Baranowski Nicholas Chapman Seth Cooper Alexandre Defelicibus Jeff Flatten Brian Koepnick Zoran Popović Bartlomiej Zaborowski David Baker Jianlin Cheng Cezary Czaplewski Alexandre Cláudio Botazzo Delbem Christodoulos Floudas Andrzej Kloczkowski Stanislaw Ołdziej Michael Levitt Harold Scheraga Chaok Seok Johannes Söding Saraswathi Vishveshwara Dong Xu Foldit Players consortium Silvia N. Crivelli |
| author_sort |
Chen Keasar |
| title |
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 |
| title_short |
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 |
| title_full |
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 |
| title_fullStr |
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 |
| title_full_unstemmed |
An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12 |
| title_sort |
analysis and evaluation of the wefold collaborative for protein structure prediction and its pipelines in casp11 and casp12 |
| publisher |
Nature Portfolio |
| publishDate |
2018 |
| url |
https://doaj.org/article/b0b847aec1154062a3c86bac14d94e55 |
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silviancrivelli analysisandevaluationofthewefoldcollaborativeforproteinstructurepredictionanditspipelinesincasp11andcasp12 |
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