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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: slusarz r. 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: slusarz r. 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.
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: slusarz r. 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.
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11.
Krupa P, Mozolewska MA, Wiśniewska M, Yin Y, He Y, Sieradzan AK, Ganzynkowicz R, Lipska AG, Karczyńska A, Ślusarz M, Ślusarz R, Giełdoń A, Czaplewski C, Jagieła D, Zaborowski B, Scheraga HA, Liwo A. Krupa P, et al. Among authors: slusarz m, slusarz r. Bioinformatics. 2016 Nov 1;32(21):3270-3278. doi: 10.1093/bioinformatics/btw404. Epub 2016 Jul 4. Bioinformatics. 2016. PMID: 27378298 Free PMC article.
Use of the UNRES force field in template-assisted prediction of protein structures and the refinement of server models: Test with CASP12 targets.
Karczyńska A, Mozolewska MA, Krupa P, Giełdoń A, Bojarski KK, Zaborowski B, Liwo A, Ślusarz R, Ślusarz M, Lee J, Joo K, Czaplewski C. Karczyńska A, et al. Among authors: slusarz m, slusarz r. J Mol Graph Model. 2018 Aug;83:92-99. doi: 10.1016/j.jmgm.2018.05.008. Epub 2018 May 24. J Mol Graph Model. 2018. PMID: 29860162
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: slusarz m, slusarz r. Sci Rep. 2018 Jul 2;8(1):9939. doi: 10.1038/s41598-018-26812-8. Sci Rep. 2018. PMID: 29967418 Free PMC article.
Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment.
Lubecka EA, Karczyńska AS, Lipska AG, Sieradzan AK, Ziȩba K, Sikorska C, Uciechowska U, Samsonov SA, Krupa P, Mozolewska MA, Golon Ł, Giełdoń A, Czaplewski C, Ślusarz R, Ślusarz M, Crivelli SN, Liwo A. Lubecka EA, et al. Among authors: slusarz m, slusarz r. J Mol Graph Model. 2019 Nov;92:154-166. doi: 10.1016/j.jmgm.2019.07.013. Epub 2019 Jul 26. J Mol Graph Model. 2019. PMID: 31376733
82 results