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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, McGuffin LJ, Wallner B, Chopra G, Adhikari B, Bhattacharya D, Blake L, Bortot LO, Cao R, Dhanasekaran BK, Dimas I, Faccioli RA, Faraggi E, Ganzynkowicz R, Ghosh S, Ghosh S, Giełdoń A, Golon L, He Y, Heo L, Hou J, Khan M, Khatib F, Khoury GA, Kieslich C, Kim DE, Krupa P, Lee GR, Li H, Li J, Lipska A, Liwo A, Maghrabi AHA, Mirdita M, Mirzaei S, Mozolewska MA, Onel M, Ovchinnikov S, Shah A, Shah U, Sidi T, Sieradzan AK, Ślusarz M, Ślusarz R, Smadbeck J, Tamamis P, Trieber N, Wirecki T, Yin Y, Zhang Y, Bacardit J, Baranowski M, Chapman N, Cooper S, Defelicibus A, Flatten J, Koepnick B, Popović Z, Zaborowski B, Baker D, Cheng J, Czaplewski C, Delbem ACB, Floudas C, Kloczkowski A, Ołdziej S, Levitt M, Scheraga H, Seok C, Söding J, Vishveshwara S, Xu D; Foldit Players consortium; Crivelli SN. Keasar C, et al. Among authors: he y. Sci Rep. 2018 Jul 2;8(1):9939. doi: 10.1038/s41598-018-26812-8. Sci Rep. 2018. PMID: 29967418 Free PMC article.
Coarse-grained force field: general folding theory.
Liwo A, He Y, Scheraga HA. Liwo A, et al. Among authors: he y. Phys Chem Chem Phys. 2011 Oct 14;13(38):16890-901. doi: 10.1039/c1cp20752k. Epub 2011 Jun 3. Phys Chem Chem Phys. 2011. PMID: 21643583 Free PMC article. Review.
WeFold: a coopetition for protein structure prediction.
Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, Bortot LO, Faccioli RA, Deng X, He Y, Krupa P, Li J, Mozolewska MA, Sieradzan AK, Smadbeck J, Wirecki T, Cooper S, Flatten J, Xu K, Baker D, Cheng J, Delbem AC, Floudas CA, Keasar C, Levitt M, Popović Z, Scheraga HA, Skolnick J, Crivelli SN; Foldit Players. Khoury GA, et al. Among authors: he y. Proteins. 2014 Sep;82(9):1850-68. doi: 10.1002/prot.24538. Epub 2014 Jul 8. Proteins. 2014. PMID: 24677212 Free PMC article.
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.
Liwo A, Baranowski M, Czaplewski C, Gołaś E, He Y, Jagieła D, Krupa P, Maciejczyk M, Makowski M, Mozolewska MA, Niadzvedtski A, Ołdziej S, Scheraga HA, Sieradzan AK, Slusarz R, Wirecki T, Yin Y, Zaborowski B. Liwo A, et al. Among authors: he y. J Mol Model. 2014 Aug;20(8):2306. doi: 10.1007/s00894-014-2306-5. Epub 2014 Jul 15. J Mol Model. 2014. PMID: 25024008 Free PMC article.
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