An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Autor: 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

Publikováno v: Scientific Reports, Vol 8, Iss 1, Pp 1-18 (2018)

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

Externí odkaz: https://doaj.org/article/b0b847aec1154062a3c86bac14d94e55

Determining crystal structures through crowdsourcing and coursework

Autor: Scott Horowitz, Brian Koepnick, Raoul Martin, Agnes Tymieniecki, Amanda A. Winburn, Seth Cooper, Jeff Flatten, David S. Rogawski, Nicole M. Koropatkin, Tsinatkeab T. Hailu, Neha Jain, Philipp Koldewey, Logan S. Ahlstrom, Matthew R. Chapman, Andrew P. Sikkema, Meredith A. Skiba, Finn P. Maloney, Felix R. M. Beinlich, Foldit Players, University of Michigan students, Zoran Popović, David Baker, Firas Khatib, James C. A. Bardwell

Publikováno v: Nature Communications, Vol 7, Iss 1, Pp 1-11 (2016)

Building crystal structures into the electron density is an important step in protein structure solution. Here, the authors recruit online game players, students, and experienced crystallographers to compete in a competition to solve a new structure,

Externí odkaz: https://doaj.org/article/b15fb233272548d7bc0404a5bf35e26f

De novo protein design by citizen scientists

Autor: Foldit Players, Gaetano T. Montelione, Matthew J. Bick, Jeff Flatten, Aaron Bauer, Brian Koepnick, Roger D. Estep, David Baker, Tamir Husain, Zoran Popović, Susan Kleinfelter, Linda Wei, Alex Ford, Toke Nørgård-Solano, Seth Cooper, Firas Khatib, Alexander Boykov, Yojiro Ishida, Gaohua Liu, Frank DiMaio, Daniel-Adriano Silva

Publikováno v: Nature

Online citizen science projects such as GalaxyZoo1, Eyewire2 and Phylo3 have proven very successful for data collection, annotation and processing, but for the most part have harnessed human pattern-recognition skills rather than human creativity. An

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::0d935a9b9943c14bb761352567920b5e
https://doi.org/10.1038/s41586-019-1274-4

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12

Autor: Shah U, Lim Heo, Renzhi Cao, Chaok Seok, Gaurav Chopra, Soma Ghosh, Phanourios Tamamis, Maghrabi Aha, Sergey Ovchinnikov, Hailong Li, Chris A. Kieslich, Dhanasekaran Bk, Milot Mirdita, Rafał Ślusarz, Adam Liwo, Kim De, Gyu Rie Lee, Michael Levitt, James Smadbeck, Blake L, Adam K. Sieradzan, Seth Cooper, Andrzej Kloczkowski, Zoran Popović, Rodrigo Antonio Faccioli, Cezary Czaplewski, Yuxin Yin, Jie Hou, Brian Koepnick, Shah A, Jilong Li, Maciej Baranowski, Chen Keasar, Yang Zhang, Delbem Acb, Magdalena A. Mozolewska, Christodoulos A. Floudas, Agnieszka G. Lipska, Badri Adhikari, Yi He, Dimas I, Leandro Oliveira Bortot, Liam J. McGuffin, Paweł Krupa, Bartłomiej Zaborowski, David Baker, Alexandre Defelicibus, Eshel Faraggi, Melis Onel, Johannes Söding, Tomasz K Wirecki, Jeff Flatten, Jianlin Cheng, Firas Khatib, Dong Xu, Silvia Crivelli, Stanisław Ołdziej, Saraswathi Vishveshwara, Debswapna Bhattacharya, Golon L, George A. Khoury, Harold A. Scheraga, Artur Giełdoń, Jaume Bacardit, Chapman N, Björn Wallner, Shokoufeh Mirzaei, Khan M, Magdalena J. Ślusarz, Tomer Sidi, Trieber N, Robert Ganzynkowicz

Publikováno v: Scientific reports, vol 8, iss 1
Repositório Institucional da USP (Biblioteca Digital da Produção Intelectual)
Universidade de São Paulo (USP)
instacron:USP
Scientific Reports
Scientific Reports, Vol 8, Iss 1, Pp 1-18 (2018)

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

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ea265f961e83f6d8e56d90a5eb07cede
https://escholarship.org/uc/item/5jp72387

WeFold: A coopetition for protein structure prediction

Autor: Leandro Oliveira Bortot, Jeffrey Skolnick, George A. Khoury, Jilong Li, David Baker, Kefan Xu, Seth Cooper, Adam Liwo, Jianlin Cheng, Xin Deng, Tomasz K Wirecki, Zoran Popović, Adam K. Sieradzan, Christodoulos A. Floudas, Jaume Bacardit, James Smadbeck, Firas Khatib, Hongyi Zhou, Alexandre C. B. Delbem, Harold A. Scheraga, Rodrigo Antonio Faccioli, Foldit Players, Chen Keasar, Jeff Flatten, Silvia Crivelli, Michael Levitt, Magdalena A. Mozolewska, Yi He, Gaurav Chopra, Paweł Krupa

Publikováno v: Proteins: Structure, Function, and Bioinformatics. 82:1850-1868

The protein structure prediction problem continues to elude scientists. Despite the introduction of many methods, only modest gains were made over the last decade for certain classes of prediction targets. To address this challenge, a social-media ba

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::a9bc8a446e9562de149f5f55cc49c663
https://doi.org/10.1002/prot.24538