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

Keasar, C and McGuffin, LJ and Wallner, B and Chopra, G and Adhikari, B and Bhattacharya, D and Blake, L and Bortot, LO and Cao, R and Dhanasekaran, BK and Dimas, I and Faccioli, RA and Faraggi, E and Ganzynkowicz, R and Ghosh, S and Ghosh, S and GieÅdoÅ, A and Golon, L and He, Y and Heo, L and Hou, J and Khan, M and Khatib, F and Khoury, GA and Kieslich, C and Kim, DE and Krupa, P and Lee, GR and Li, H and Li, J and Lipska, A and Liwo, A and Maghrabi, AHA and Mirdita, M and Mirzaei, S and Mozolewska, MA and Onel, M and Ovchinnikov, S and Shah, A and Shah, U and Sidi, T and Sieradzan, AK and Å�lusarz, M and Å�lusarz, R and Smadbeck, J and Tamamis, P and Trieber, N and Wirecki, T and Yin, Y and Zhang, Y and Bacardit, J and Baranowski, M and Chapman, N and Cooper, S and Defelicibus, A and Flatten, J and Koepnick, B and PopoviÄ�, Z and Zaborowski, B and Baker, D and Cheng, J and Czaplewski, C and Delbem, ACB and Floudas, C and Kloczkowski, A and OÅ�dziej, S and Levitt, M and Scheraga, H and Seok, C and Söding, J and Vishveshwara, S and Xu, D and Caglar, A and Coral, A and MacMillan, A and Lubow, A and Failer, B and Kestemont, B and Landers, CR and Painter, CR and Garnier, C and Sellin, C and Janz, D and Wheeler, DC and Simon, V and Flear, DM and Croze, E and McIlvaine, GV and Beecher, G and Lawrie, G and Ykman, G and Feldmann, H and Fuentes, HK and Terumasa, H and Kovanecz, I and Longino, III and Nijland, JH and Diderich, JA and Canfield, JM and Eriksson, J and Slone, JD and Appel, JG and Mitchell, J and Mitch, J and Loots-Boiy, J and Brownlee, JM and Wilson, K and Clayton, KT and Deford, KE and Abbey, KJ and Withers, L and Wei, L and Ives, L and Miller, LA and Carpenter, L and Sharma, MG and Ricci, M and Binfield, MS and Davids, MJ and Gaebel, M and Cassidy, MD and Fagiola, M and Pfützenreuter, M and Barlow, N and Triggiani, IV and Innes, RBM and Leduc, R and Dos Santos Gomes, RLC and Morneau, RLR and Zaccanelli, SJ and Kleinfelter, SC and Van Der Laan, TJA and Bausewein, T and George, TJ and Mikhail, V and Barmettler, W and Crivelli, SN (2018) An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12. In: Scientific Reports, 8 (1).

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Official URL: https://doi.org/10.1038/s41598-018-26812-8


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.

Item Type: Journal Article
Publication: Scientific Reports
Publisher: Nature Publishing Group
Additional Information: The copyright for this article belongs to the Authors.
Keywords: CASP12 protein, human; caspase; caspase 11, human; caspase 12, biology; chemistry; comparative study; human; metabolism; molecular model; procedures; protein conformation; software, Caspase 12; Caspases; Computational Biology; Humans; Models, Molecular; Protein Conformation; Software
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Date Deposited: 23 Aug 2022 10:04
Last Modified: 23 Aug 2022 10:04
URI: https://eprints.iisc.ac.in/id/eprint/76202

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