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

Drugit: Crowd-sourcing molecular design of non-peptidic VHL binders

Autor: Thomas Scott, Christian Alan Paul Smethurst, Yvonne Westermaier, Moriz Mayer, Peter Greb, Roland Kousek, Tobias Biberger, Gerd Bader, Zuzana Jandova, Philipp S. Schmalhorst, Julian E. Fuchs, Aniket Magarkar, Christoph Hoenke, Thomas Gerstberger, Steven A. Combs, Richard Pape, Saksham Phul, Sandeepkumar Kothiwale, Andreas Bergner, Alex G. Waterson, Foldit Players, Harald Weinstabl, Darryl B. McConnell, Jark Böttcher, Jens Meiler, Rocco Moretti

Given the role of human intuition in current drug design efforts, crowd-sourced 'citizen scientist' games have the potential to greatly expand the pool of potential drug designers. Here, we introduce ‘Drugit', the small molecule design mode of the

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::287b3949d9d0ebf819f483d064d56529
https://doi.org/10.26434/chemrxiv-2023-lczzd

Protein sequence design by conformational landscape optimization

Autor: Basile I. M. Wicky, David D. Kim, Foldit Players, Sergey Ovchinnikov, Doug Tischer, David Juergens, David Baker, Christoffer Norn, Brian Koepnick, Ivan Anishchenko, Sirui Liu

Publikováno v: Proceedings of the National Academy of Sciences of the United States of America

Significance Almost all proteins fold to their lowest free energy state, which is determined by their amino acid sequence. Computational protein design has primarily focused on finding sequences that have very low energy in the target designed struct

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::378e9cc6474b19e3d999088d83cac12d
https://pubmed.ncbi.nlm.nih.gov/33712545

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