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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: slusarz r. Proteins. 2023 Dec;91(12):1658-1683. doi: 10.1002/prot.26609. Epub 2023 Oct 31. Proteins. 2023. PMID: 37905971 Free PMC article.
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.
Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.
Karczyńska AS, Ziȩba K, Uciechowska U, Mozolewska MA, Krupa P, Lubecka EA, Lipska AG, Sikorska C, Samsonov SA, Sieradzan AK, Giełdoń A, Liwo A, Ślusarz R, Ślusarz M, Lee J, Joo K, Czaplewski C. Karczyńska AS, et al. Among authors: slusarz m, slusarz r. J Chem Inf Model. 2020 Mar 23;60(3):1844-1864. doi: 10.1021/acs.jcim.9b00864. Epub 2020 Feb 11. J Chem Inf Model. 2020. PMID: 31999919 Free PMC article.
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: slusarz r, slusarz mj. 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
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
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
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.
82 results