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Items: 11

1.

Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI rounds 37-45.

Roy Burman SS, Nance ML, Jeliazkov JR, Labonte JW, Lubin JH, Biswas N, Gray JJ.

Proteins. 2019 Nov 19. doi: 10.1002/prot.25855. [Epub ahead of print]

PMID:
31742764
2.

Toward the computational design of protein crystals with improved resolution.

Jeliazkov JR, Robinson AC, García-Moreno E B, Berger JM, Gray JJ.

Acta Crystallogr D Struct Biol. 2019 Nov 1;75(Pt 11):1015-1027. doi: 10.1107/S2059798319013226. Epub 2019 Nov 1.

PMID:
31692475
3.

Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation.

Santiago-Frangos A, Fröhlich KS, Jeliazkov JR, Małecka EM, Marino G, Gray JJ, Luisi BF, Woodson SA, Hardwick SW.

Proc Natl Acad Sci U S A. 2019 May 28;116(22):10978-10987. doi: 10.1073/pnas.1814428116. Epub 2019 May 10.

4.

Non-H3 CDR template selection in antibody modeling through machine learning.

Long X, Jeliazkov JR, Gray JJ.

PeerJ. 2019 Jan 11;7:e6179. doi: 10.7717/peerj.6179. eCollection 2019.

5.

Plasma Cells Are the Most Abundant Gluten Peptide MHC-expressing Cells in Inflamed Intestinal Tissues From Patients With Celiac Disease.

Høydahl LS, Richter L, Frick R, Snir O, Gunnarsen KS, Landsverk OJB, Iversen R, Jeliazkov JR, Gray JJ, Bergseng E, Foss S, Qiao SW, Lundin KEA, Jahnsen J, Jahnsen FL, Sandlie I, Sollid LM, Løset GÅ.

Gastroenterology. 2019 Apr;156(5):1428-1439.e10. doi: 10.1053/j.gastro.2018.12.013. Epub 2018 Dec 26.

PMID:
30593798
6.

Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification.

Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Katoh N, Tsumoto K, Gray JJ.

Front Immunol. 2018 Mar 2;9:413. doi: 10.3389/fimmu.2018.00413. eCollection 2018.

7.

Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors.

Kalin JH, Wu M, Gomez AV, Song Y, Das J, Hayward D, Adejola N, Wu M, Panova I, Chung HJ, Kim E, Roberts HJ, Roberts JM, Prusevich P, Jeliazkov JR, Roy Burman SS, Fairall L, Milano C, Eroglu A, Proby CM, Dinkova-Kostova AT, Hancock WW, Gray JJ, Bradner JE, Valente S, Mai A, Anders NM, Rudek MA, Hu Y, Ryu B, Schwabe JWR, Mattevi A, Alani RM, Cole PA.

Nat Commun. 2018 Jan 4;9(1):53. doi: 10.1038/s41467-017-02242-4.

8.

Acidic C-terminal domains autoregulate the RNA chaperone Hfq.

Santiago-Frangos A, Jeliazkov JR, Gray JJ, Woodson SA.

Elife. 2017 Aug 9;6. pii: e27049. doi: 10.7554/eLife.27049.

9.

The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.

Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL Jr, Das R, Baker D, Kuhlman B, Kortemme T, Gray JJ.

J Chem Theory Comput. 2017 Jun 13;13(6):3031-3048. doi: 10.1021/acs.jctc.7b00125. Epub 2017 May 12.

10.

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.

11.

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.

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