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Computational redesign of a fluorogen activating protein with Rosetta.
Bozhanova NG, Harp JM, Bender BJ, Gavrikov AS, Gorbachev DA, Baranov MS, Mercado CB, Zhang X, Lukyanov KA, Mishin AS, Meiler J. Bozhanova NG, et al. Among authors: bender bj. PLoS Comput Biol. 2021 Nov 8;17(11):e1009555. doi: 10.1371/journal.pcbi.1009555. eCollection 2021 Nov. PLoS Comput Biol. 2021. PMID: 34748541 Free PMC article.
Rosetta and the Design of Ligand Binding Sites.
Moretti R, Bender BJ, Allison B, Meiler J. Moretti R, et al. Among authors: bender bj. Methods Mol Biol. 2016;1414:47-62. doi: 10.1007/978-1-4939-3569-7_4. Methods Mol Biol. 2016. PMID: 27094285 Free PMC article.
Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.
Bender BJ, Cisneros A 3rd, Duran AM, Finn JA, Fu D, Lokits AD, Mueller BK, Sangha AK, Sauer MF, Sevy AM, Sliwoski G, Sheehan JH, DiMaio F, Meiler J, Moretti R. Bender BJ, et al. Biochemistry. 2016 Aug 30;55(34):4748-63. doi: 10.1021/acs.biochem.6b00444. Epub 2016 Aug 16. Biochemistry. 2016. PMID: 27490953 Free PMC article. Review.
Improved in Vitro Folding of the Y2 G Protein-Coupled Receptor into Bicelles.
Schmidt P, Bender BJ, Kaiser A, Gulati K, Scheidt HA, Hamm HE, Meiler J, Beck-Sickinger AG, Huster D. Schmidt P, et al. Among authors: bender bj. Front Mol Biosci. 2018 Jan 17;4:100. doi: 10.3389/fmolb.2017.00100. eCollection 2017. Front Mol Biosci. 2018. PMID: 29387686 Free PMC article.
Structural basis of ligand binding modes at the neuropeptide Y Y1 receptor.
Yang Z, Han S, Keller M, Kaiser A, Bender BJ, Bosse M, Burkert K, Kögler LM, Wifling D, Bernhardt G, Plank N, Littmann T, Schmidt P, Yi C, Li B, Ye S, Zhang R, Xu B, Larhammar D, Stevens RC, Huster D, Meiler J, Zhao Q, Beck-Sickinger AG, Buschauer A, Wu B. Yang Z, et al. Among authors: bender bj. Nature. 2018 Apr;556(7702):520-524. doi: 10.1038/s41586-018-0046-x. Epub 2018 Apr 18. Nature. 2018. PMID: 29670288 Free PMC article.
Modeling the complete chemokine-receptor interaction.
Wedemeyer MJ, Mueller BK, Bender BJ, Meiler J, Volkman BF. Wedemeyer MJ, et al. Among authors: bender bj. Methods Cell Biol. 2019;149:289-314. doi: 10.1016/bs.mcb.2018.09.005. Epub 2018 Nov 1. Methods Cell Biol. 2019. PMID: 30616825 Free PMC article.
Structural Model of Ghrelin Bound to its G Protein-Coupled Receptor.
Bender BJ, Vortmeier G, Ernicke S, Bosse M, Kaiser A, Els-Heindl S, Krug U, Beck-Sickinger A, Meiler J, Huster D. Bender BJ, et al. Structure. 2019 Mar 5;27(3):537-544.e4. doi: 10.1016/j.str.2018.12.004. Epub 2019 Jan 24. Structure. 2019. PMID: 30686667 Free PMC article.
Macromolecular modeling and design in Rosetta: recent methods and frameworks.
Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. Leman JK, et al. Among authors: bender bj. Nat Methods. 2020 Jul;17(7):665-680. doi: 10.1038/s41592-020-0848-2. Epub 2020 Jun 1. Nat Methods. 2020. PMID: 32483333 Free PMC article. Review.
26 results