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Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.
Lensink MF, Brysbaert G, Mauri T, Nadzirin N, Velankar S, Chaleil RAG, Clarence T, Bates PA, Kong R, Liu B, Yang G, Liu M, Shi H, Lu X, Chang S, Roy RS, Quadir F, Liu J, Cheng J, Antoniak A, Czaplewski C, Giełdoń A, Kogut M, Lipska AG, Liwo A, Lubecka EA, Maszota-Zieleniak M, Sieradzan AK, Ślusarz R, Wesołowski PA, Zięba K, Del Carpio Muñoz CA, Ichiishi E, Harmalkar A, Gray JJ, Bonvin AMJJ, Ambrosetti F, Vargas Honorato R, Jandova Z, Jiménez-García B, Koukos PI, Van Keulen S, Van Noort CW, Réau M, Roel-Touris J, Kotelnikov S, Padhorny D, Porter KA, Alekseenko A, Ignatov M, Desta I, Ashizawa R, Sun Z, Ghani U, Hashemi N, Vajda S, Kozakov D, Rosell M, Rodríguez-Lumbreras LA, Fernandez-Recio J, Karczynska A, Grudinin S, Yan Y, Li H, Lin P, Huang SY, Christoffer C, Terashi G, Verburgt J, Sarkar D, Aderinwale T, Wang X, Kihara D, Nakamura T, Hanazono Y, Gowthaman R, Guest JD, Yin R, Taherzadeh G, Pierce BG, Barradas-Bautista D, Cao Z, Cavallo L, Oliva R, Sun Y, Zhu S, Shen Y, Park T, Woo H, Yang J, Kwon S, Won J, Seok C, Kiyota Y, Kobayashi S, Harada Y, Takeda-Shitaka M, Kundrotas PJ, Singh A, Vakser IA, Dapkūnas J, Olechnovič K, Venclovas Č, Duan R, Qiu L, Xu X, Zhang S, Zou X,… See abstract for full author list ➔ Lensink MF, et al. Among authors: sieradzan ak. Proteins. 2021 Dec;89(12):1800-1823. doi: 10.1002/prot.26222. Epub 2021 Sep 13. Proteins. 2021. PMID: 34453465 Free PMC article.
Lessons from application of the UNRES force field to predictions of structures of CASP10 targets.
He Y, Mozolewska MA, Krupa P, Sieradzan AK, Wirecki TK, Liwo A, Kachlishvili K, Rackovsky S, Jagiela D, Ślusarz R, Czaplewski CR, Ołdziej S, Scheraga HA. He Y, et al. Among authors: sieradzan ak. Proc Natl Acad Sci U S A. 2013 Sep 10;110(37):14936-41. doi: 10.1073/pnas.1313316110. Epub 2013 Aug 26. Proc Natl Acad Sci U S A. 2013. PMID: 23980156 Free PMC article.
Folding and self-assembly of a small protein complex.
Sieradzan AK, Liwo A, Hansmann UH. Sieradzan AK, et al. J Chem Theory Comput. 2012 Sep 11;8(9):3416-3422. doi: 10.1021/ct300528r. J Chem Theory Comput. 2012. PMID: 24039552 Free PMC article.
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: sieradzan ak. 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: sieradzan ak. 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.
80 results