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Items: 7

1.

Efficient flexible backbone protein-protein docking for challenging targets.

Marze NA, Roy Burman SS, Sheffler W, Gray JJ.

Bioinformatics. 2018 Oct 15;34(20):3461-3469. doi: 10.1093/bioinformatics/bty355.

2.

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.

Nat Protoc. 2017 Feb;12(2):401-416. doi: 10.1038/nprot.2016.180. Epub 2017 Jan 26.

3.

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.

Proteins. 2017 Mar;85(3):479-486. doi: 10.1002/prot.25168. Epub 2016 Oct 24.

4.

Improved prediction of antibody VL-VH orientation.

Marze NA, Lyskov S, Gray JJ.

Protein Eng Des Sel. 2016 Oct;29(10):409-418. doi: 10.1093/protein/gzw013. Epub 2016 Jun 8.

5.

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.

Proteins. 2016 Sep;84 Suppl 1:323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1.

6.

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.

PLoS One. 2015 Dec 28;10(12):e0145850. doi: 10.1371/journal.pone.0145850. eCollection 2015.

7.

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.

Proteins. 2014 Aug;82(8):1611-23. doi: 10.1002/prot.24534. Epub 2014 Mar 31.

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