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Items: 1 to 50 of 245

1.

Chiral switching in biomineral suprastructures induced by homochiral l-amino acid.

Jiang W, Pacella MS, Vali H, Gray JJ, McKee MD.

Sci Adv. 2018 Aug 1;4(8):eaas9819. doi: 10.1126/sciadv.aas9819. eCollection 2018 Aug.

2.

Modulation of calcium oxalate dihydrate growth by phosphorylated osteopontin peptides.

Chien YC, Mansouri A, Jiang W, Khan SR, Gray JJ, McKee MD.

J Struct Biol. 2018 Nov;204(2):131-144. doi: 10.1016/j.jsb.2018.07.010. Epub 2018 Jul 17.

PMID:
30016645
3.

Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell.

Athanasiadou D, Jiang W, Goldbaum D, Saleem A, Basu K, Pacella MS, Böhm CF, Chromik RR, Hincke MT, Rodríguez-Navarro AB, Vali H, Wolf SE, Gray JJ, Bui KH, McKee MD.

Sci Adv. 2018 Mar 30;4(3):eaar3219. doi: 10.1126/sciadv.aar3219. eCollection 2018 Mar.

4.

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.

PMID:
29718115
5.

A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces.

Lubin JH, Pacella MS, Gray JJ.

Langmuir. 2018 May 8;34(18):5279-5289. doi: 10.1021/acs.langmuir.8b00212. Epub 2018 Apr 26.

PMID:
29630384
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.

The Bcl-2 Homology-3 Domain (BH3)-Only Proteins, Bid, DP5/Hrk, and BNip3L, Are Upregulated in Reactive Astrocytes of End-Stage Mutant SOD1 Mouse Spinal Cord.

Duval N, Sumner WA, Andrianakos AG, Gray JJ, Bouchard RJ, Wilkins HM, Linseman DA.

Front Cell Neurosci. 2018 Jan 30;12:15. doi: 10.3389/fncel.2018.00015. eCollection 2018.

8.

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.

9.

A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.

Alford RF, Leaver-Fay A, Gonzales L, Dolan EL, Gray JJ.

PLoS Comput Biol. 2017 Dec 7;13(12):e1005837. doi: 10.1371/journal.pcbi.1005837. eCollection 2017 Dec.

10.

Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.

Koehler Leman J, D'Avino AR, Bhatnagar Y, Gray JJ.

Proteins. 2018 Jan;86(1):57-74. doi: 10.1002/prot.25402. Epub 2017 Nov 8.

PMID:
29044728
11.

Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).

Moretti R, Lyskov S, Das R, Meiler J, Gray JJ.

Protein Sci. 2018 Jan;27(1):259-268. doi: 10.1002/pro.3313. Epub 2017 Oct 27.

PMID:
28960691
12.

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.

13.

Structure-based cross-docking analysis of antibody-antigen interactions.

Kilambi KP, Gray JJ.

Sci Rep. 2017 Aug 15;7(1):8145. doi: 10.1038/s41598-017-08414-y.

14.

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.

15.

Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate.

Jiang W, Pacella MS, Athanasiadou D, Nelea V, Vali H, Hazen RM, Gray JJ, McKee MD.

Nat Commun. 2017 Apr 13;8:15066. doi: 10.1038/ncomms15066.

16.

Glycoengineering of Esterase Activity through Metabolic Flux-Based Modulation of Sialic Acid.

Mathew MP, Tan E, Labonte JW, Shah S, Saeui CT, Liu L, Bhattacharya R, Bovonratwet P, Gray JJ, Yarema KJ.

Chembiochem. 2017 Jul 4;18(13):1204-1215. doi: 10.1002/cbic.201600698. Epub 2017 Apr 20.

17.

A high throughput mutagenic analysis of yeast sumo structure and function.

Newman HA, Meluh PB, Lu J, Vidal J, Carson C, Lagesse E, Gray JJ, Boeke JD, Matunis MJ.

PLoS Genet. 2017 Feb 6;13(2):e1006612. doi: 10.1371/journal.pgen.1006612. eCollection 2017 Feb.

18.

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.

19.

Expanding the toolkit for membrane protein modeling in Rosetta.

Koehler Leman J, Mueller BK, Gray JJ.

Bioinformatics. 2017 Mar 1;33(5):754-756. doi: 10.1093/bioinformatics/btw716.

20.

Residue-centric modeling and design of saccharide and glycoconjugate structures.

Labonte JW, Adolf-Bryfogle J, Schief WR, Gray JJ.

J Comput Chem. 2017 Feb 15;38(5):276-287. doi: 10.1002/jcc.24679. Epub 2016 Nov 30. Erratum in: J Comput Chem. 2017 May 15;38(13):1015.

21.

Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint.

Weitzner BD, Gray JJ.

J Immunol. 2017 Jan 1;198(1):505-515. Epub 2016 Nov 21.

22.

Structural Diversity in the Type IV Pili of Multidrug-resistant Acinetobacter.

Piepenbrink KH, Lillehoj E, Harding CM, Labonte JW, Zuo X, Rapp CA, Munson RS Jr, Goldblum SE, Feldman MF, Gray JJ, Sundberg EJ.

J Biol Chem. 2016 Oct 28;291(44):22924-22935. Epub 2016 Sep 15.

23.

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.

24.

Pushing the Backbone in Protein-Protein Docking.

Kuroda D, Gray JJ.

Structure. 2016 Oct 4;24(10):1821-1829. doi: 10.1016/j.str.2016.06.025. Epub 2016 Aug 25.

25.

Norovirus Gastroenteritis in a Birth Cohort in Southern India.

Menon VK, George S, Sarkar R, Giri S, Samuel P, Vivek R, Saravanabavan A, Liakath FB, Ramani S, Iturriza-Gomara M, Gray JJ, Brown DW, Estes MK, Kang G.

PLoS One. 2016 Jun 10;11(6):e0157007. doi: 10.1371/journal.pone.0157007. eCollection 2016.

26.

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.

27.

Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking.

Kuroda D, Gray JJ.

Bioinformatics. 2016 Aug 15;32(16):2451-6. doi: 10.1093/bioinformatics/btw197. Epub 2016 Apr 19.

28.

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.

29.

Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires.

DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D, Ellington AD, Ippolito GC, Gray JJ, Georgiou G.

Proc Natl Acad Sci U S A. 2016 May 10;113(19):E2636-45. doi: 10.1073/pnas.1525510113. Epub 2016 Apr 25.

30.

A Comprehensive, High-Resolution Map of a Gene's Fitness Landscape.

Firnberg E, Labonte JW, Gray JJ, Ostermeier M.

Mol Biol Evol. 2016 May;33(5):1378. doi: 10.1093/molbev/msw021. Epub 2016 Feb 23. No abstract available.

31.

Viral infection causes a shift in the self peptide repertoire presented by human MHC class I molecules.

Spencer CT, Bezbradica JS, Ramos MG, Arico CD, Conant SB, Gilchuk P, Gray JJ, Zheng M, Niu X, Hildebrand W, Link AJ, Joyce S.

Proteomics Clin Appl. 2015 Dec;9(11-12):1035-52. doi: 10.1002/prca.201500106.

32.

Molecular Determinants for Protein Stabilization by Insertional Fusion to a Thermophilic Host Protein.

Pierre B, Labonte JW, Xiong T, Aoraha E, Williams A, Shah V, Chau E, Helal KY, Gray JJ, Kim JR.

Chembiochem. 2015 Nov 2;16(16):2392-402. doi: 10.1002/cbic.201500310. Epub 2015 Sep 22.

PMID:
26391210
33.

An Integrated Framework Advancing Membrane Protein Modeling and Design.

Alford RF, Koehler Leman J, Weitzner BD, Duran AM, Tilley DC, Elazar A, Gray JJ.

PLoS Comput Biol. 2015 Sep 1;11(9):e1004398. doi: 10.1371/journal.pcbi.1004398. eCollection 2015 Sep.

34.

Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to Hirschsprung disease liability.

Jiang Q, Arnold S, Heanue T, Kilambi KP, Doan B, Kapoor A, Ling AY, Sosa MX, Guy M, Jiang Q, Burzynski G, West K, Bessling S, Griseri P, Amiel J, Fernandez RM, Verheij JB, Hofstra RM, Borrego S, Lyonnet S, Ceccherini I, Gray JJ, Pachnis V, McCallion AS, Chakravarti A.

Am J Hum Genet. 2015 Apr 2;96(4):581-96. doi: 10.1016/j.ajhg.2015.02.014.

35.

The origin of CDR H3 structural diversity.

Weitzner BD, Dunbrack RL Jr, Gray JJ.

Structure. 2015 Feb 3;23(2):302-11. doi: 10.1016/j.str.2014.11.010. Epub 2015 Jan 8.

36.

Protein-protein docking with dynamic residue protonation states.

Kilambi KP, Reddy K, Gray JJ.

PLoS Comput Biol. 2014 Dec 11;10(12):e1004018. doi: 10.1371/journal.pcbi.1004018. eCollection 2014 Dec.

37.

C-terminal binding proteins: central players in development and disease.

Stankiewicz TR, Gray JJ, Winter AN, Linseman DA.

Biomol Concepts. 2014 Dec;5(6):489-511. doi: 10.1515/bmc-2014-0027. Review.

PMID:
25429601
38.

Computational modeling of membrane proteins.

Koehler Leman J, Ulmschneider MB, Gray JJ.

Proteins. 2015 Jan;83(1):1-24. doi: 10.1002/prot.24703. Epub 2014 Nov 19. Review.

39.

Stable over-expression of the 2-oxoglutarate carrier enhances neuronal cell resistance to oxidative stress via Bcl-2-dependent mitochondrial GSH transport.

Wilkins HM, Brock S, Gray JJ, Linseman DA.

J Neurochem. 2014 Jul;130(1):75-86. doi: 10.1111/jnc.12709. Epub 2014 Apr 2.

40.

A comprehensive, high-resolution map of a gene's fitness landscape.

Firnberg E, Labonte JW, Gray JJ, Ostermeier M.

Mol Biol Evol. 2014 Jun;31(6):1581-92. doi: 10.1093/molbev/msu081. Epub 2014 Feb 23. Erratum in: Mol Biol Evol. 2016 May;33(5):1378.

41.

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.

42.

Using the RosettaSurface algorithm to predict protein structure at mineral surfaces.

Pacella MS, Koo da CE, Thottungal RA, Gray JJ.

Methods Enzymol. 2013;532:343-66. doi: 10.1016/B978-0-12-416617-2.00016-3. Review.

43.

Blind prediction of interfacial water positions in CAPRI.

Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ.

Proteins. 2014 Apr;82(4):620-32. doi: 10.1002/prot.24439. Epub 2013 Nov 23.

44.

Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27.

Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ.

Proteins. 2013 Dec;81(12):2201-9. doi: 10.1002/prot.24425. Epub 2013 Oct 17.

45.

Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design.

Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, Kirshenbaum K, Arora PS, Das R, Bonneau R.

PLoS One. 2013 Jul 15;8(7):e67051. doi: 10.1371/journal.pone.0067051. Print 2013.

46.

Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.

Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D.

Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23.

47.

Universal extraction method for gastrointestinal pathogens.

Halstead FD, Lee AV, Couto-Parada X, Polley SD, Ling C, Jenkins C, Chalmers RM, Elwin K, Gray JJ, Iturriza-Gómara M, Wain J, Clark DA, Bolton FJ, Manuel RJ; Olympics GI Group.

J Med Microbiol. 2013 Oct;62(Pt 10):1535-9. doi: 10.1099/jmm.0.058743-0. Epub 2013 Jul 5.

PMID:
23831766
48.

Rotavirus shedding in symptomatic and asymptomatic children using reverse transcription-quantitative PCR.

Mukhopadhya I, Sarkar R, Menon VK, Babji S, Paul A, Rajendran P, Sowmyanarayanan TV, Moses PD, Iturriza-Gomara M, Gray JJ, Kang G.

J Med Virol. 2013 Sep;85(9):1661-8. doi: 10.1002/jmv.23641. Epub 2013 Jun 17.

49.

Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability.

Der BS, Kluwe C, Miklos AE, Jacak R, Lyskov S, Gray JJ, Georgiou G, Ellington AD, Kuhlman B.

PLoS One. 2013 May 31;8(5):e64363. doi: 10.1371/journal.pone.0064363. Print 2013.

50.

Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).

Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, Gray JJ, Das R.

PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013.

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