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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: christoffer cw. Proteins. 2023 Dec;91(12):1658-1683. doi: 10.1002/prot.26609. Epub 2023 Oct 31. Proteins. 2023. PMID: 37905971 Free PMC article.
RL-MLZerD: Multimeric protein docking using reinforcement learning.
Aderinwale T, Christoffer C, Kihara D. Aderinwale T, et al. Among authors: christoffer c. Front Mol Biosci. 2022 Aug 26;9:969394. doi: 10.3389/fmolb.2022.969394. eCollection 2022. Front Mol Biosci. 2022. PMID: 36090027 Free PMC article.
LZerD webserver for pairwise and multiple protein-protein docking.
Christoffer C, Chen S, Bharadwaj V, Aderinwale T, Kumar V, Hormati M, Kihara D. Christoffer C, et al. Nucleic Acids Res. 2021 Jul 2;49(W1):W359-W365. doi: 10.1093/nar/gkab336. Nucleic Acids Res. 2021. PMID: 33963854 Free PMC article.
Surface-based protein domains retrieval methods from a SHREC2021 challenge.
Langenfeld F, Aderinwale T, Christoffer C, Shin WH, Terashi G, Wang X, Kihara D, Benhabiles H, Hammoudi K, Cabani A, Windal F, Melkemi M, Otu E, Zwiggelaar R, Hunter D, Liu Y, Sirugue L, Nguyen HH, Nguyen TH, Nguyen-Truong VT, Le D, Nguyen HD, Tran MT, Montès M. Langenfeld F, et al. Among authors: christoffer c. J Mol Graph Model. 2022 Mar;111:108103. doi: 10.1016/j.jmgm.2021.108103. Epub 2021 Dec 21. J Mol Graph Model. 2022. PMID: 34959149 Free PMC article.
A global map of the protein shape universe.
Han X, Sit A, Christoffer C, Chen S, Kihara D. Han X, et al. Among authors: christoffer c. PLoS Comput Biol. 2019 Apr 12;15(4):e1006969. doi: 10.1371/journal.pcbi.1006969. eCollection 2019 Apr. PLoS Comput Biol. 2019. PMID: 30978181 Free PMC article.
30 results