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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment.
Lensink MF, Brysbaert G, Raouraoua N, Bates PA, Giulini M, Honorato RV, van Noort C, Teixeira JMC, Bonvin AMJJ, Kong R, Shi H, Lu X, Chang S, Liu J, Guo Z, Chen X, Morehead A, Roy RS, Wu T, Giri N, Quadir F, Chen C, Cheng J, Del Carpio CA, Ichiishi E, Rodriguez-Lumbreras LA, Fernandez-Recio J, Harmalkar A, Chu LS, Canner S, Smanta R, Gray JJ, Li H, Lin P, He J, Tao H, Huang SY, Roel-Touris J, Jimenez-Garcia B, Christoffer CW, Jain AJ, Kagaya Y, Kannan H, Nakamura T, Terashi G, Verburgt JC, Zhang Y, Zhang Z, Fujuta H, Sekijima M, Kihara D, Khan O, Kotelnikov S, Ghani U, Padhorny D, Beglov D, Vajda S, Kozakov D, Negi SS, Ricciardelli T, Barradas-Bautista D, Cao Z, Chawla M, Cavallo L, Oliva R, Yin R, Cheung M, Guest JD, Lee J, Pierce BG, Shor B, Cohen T, Halfon M, Schneidman-Duhovny D, Zhu S, Yin R, Sun Y, Shen Y, Maszota-Zieleniak M, Bojarski KK, Lubecka EA, Marcisz M, Danielsson A, Dziadek L, Gaardlos M, Gieldon A, Liwo A, Samsonov SA, Slusarz R, Zieba K, Sieradzan AK, Czaplewski C, Kobayashi S, Miyakawa Y, Kiyota Y, Takeda-Shitaka M, Olechnovic K, Valancauskas L, Dapkunas J, Venclovas C, Wallner B, Yang L, Hou C, He X, Guo S, Jiang S, Ma X, Duan R, Qui L, Xu X, Zou X, Vela… See abstract for full author list ➔ Lensink MF, et al. Among authors: bojarski kk. Proteins. 2023 Dec;91(12):1658-1683. doi: 10.1002/prot.26609. Epub 2023 Oct 31. Proteins. 2023. PMID: 37905971 Free PMC article.
Molecular dynamics-based model of VEGF-A and its heparin interactions.
Uciechowska-Kaczmarzyk U, Babik S, Zsila F, Bojarski KK, Beke-Somfai T, Samsonov SA. Uciechowska-Kaczmarzyk U, et al. J Mol Graph Model. 2018 Jun;82:157-166. doi: 10.1016/j.jmgm.2018.04.015. Epub 2018 Apr 27. J Mol Graph Model. 2018. PMID: 29738889
Rat cathepsin K: Enzymatic specificity and regulation of its collagenolytic activity.
Lecaille F, Chazeirat T, Bojarski KK, Renault J, Saidi A, Prasad VGNV, Samsonov S, Lalmanach G. Lecaille F, et al. Among authors: bojarski kk. Biochim Biophys Acta Proteins Proteom. 2020 Feb;1868(2):140318. doi: 10.1016/j.bbapap.2019.140318. Epub 2019 Nov 15. Biochim Biophys Acta Proteins Proteom. 2020. PMID: 31740411
Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment.
Antoniak A, Biskupek I, Bojarski KK, Czaplewski C, Giełdoń A, Kogut M, Kogut MM, Krupa P, Lipska AG, Liwo A, Lubecka EA, Marcisz M, Maszota-Zieleniak M, Samsonov SA, Sieradzan AK, Ślusarz MJ, Ślusarz R, Wesołowski PA, Ziȩba K. Antoniak A, et al. Among authors: bojarski kk. J Mol Graph Model. 2021 Nov;108:108008. doi: 10.1016/j.jmgm.2021.108008. Epub 2021 Aug 17. J Mol Graph Model. 2021. PMID: 34419932
The abnormal accumulation of heparan sulfate in patients with mucopolysaccharidosis prevents the elastolytic activity of cathepsin V.
Chazeirat T, Denamur S, Bojarski KK, Andrault PM, Sizaret D, Zhang F, Saidi A, Tardieu M, Linhardt RJ, Labarthe F, Brömme D, Samsonov SA, Lalmanach G, Lecaille F. Chazeirat T, et al. Among authors: bojarski kk. Carbohydr Polym. 2021 Feb 1;253:117261. doi: 10.1016/j.carbpol.2020.117261. Epub 2020 Oct 20. Carbohydr Polym. 2021. PMID: 33278943
13 results