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Macromolecular modeling and design in Rosetta: recent methods and frameworks.
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.
Modeling and docking of antibody structures with Rosetta.
Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL Jr, Gray JJ.
Weitzner BD, et al.
Nat Protoc. 2017 Feb;12(2):401-416. doi: 10.1038/nprot.2016.180. Epub 2017 Jan 26.
Nat Protoc. 2017.
PMID: 28125104
Free PMC article.
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Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35.
Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE, DiMaio F, Gray JJ.
Marze NA, et al.
Proteins. 2017 Mar;85(3):479-486. doi: 10.1002/prot.25168. Epub 2016 Oct 24.
Proteins. 2017.
PMID: 27667482
Free PMC article.
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Efficient flexible backbone protein-protein docking for challenging targets.
Marze NA, Roy Burman SS, Sheffler W, Gray JJ.
Marze NA, et al.
Bioinformatics. 2018 Oct 15;34(20):3461-3469. doi: 10.1093/bioinformatics/bty355.
Bioinformatics. 2018.
PMID: 29718115
Free PMC article.
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Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization.
Weitzner BD, Kuroda D, Marze N, Xu J, Gray JJ.
Weitzner BD, et al.
Proteins. 2014 Aug;82(8):1611-23. doi: 10.1002/prot.24534. Epub 2014 Mar 31.
Proteins. 2014.
PMID: 24519881
Free PMC article.
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Improved prediction of antibody VL-VH orientation.
Marze NA, Lyskov S, Gray JJ.
Marze NA, et al.
Protein Eng Des Sel. 2016 Oct;29(10):409-418. doi: 10.1093/protein/gzw013. Epub 2016 Jun 8.
Protein Eng Des Sel. 2016.
PMID: 27276984
Free PMC article.
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Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RA, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ichiishi E, Marze N, Kuroda D, Roy Burman SS, Gray JJ, Chermak E, Cavallo L, Oliva R, Tovchigrechko A, Wodak SJ.
Lensink MF, et al.
Proteins. 2016 Sep;84 Suppl 1(Suppl Suppl 1):323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.
Proteins. 2016.
PMID: 27122118
Free PMC article.
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Catabolism of Branched Chain Amino Acids Contributes Significantly to Synthesis of Odd-Chain and Even-Chain Fatty Acids in 3T3-L1 Adipocytes.
Crown SB, Marze N, Antoniewicz MR.
Crown SB, et al.
PLoS One. 2015 Dec 28;10(12):e0145850. doi: 10.1371/journal.pone.0145850. eCollection 2015.
PLoS One. 2015.
PMID: 26710334
Free PMC article.
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