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Items: 24

1.

De novo design of self-assembling helical protein filaments.

Shen H, Fallas JA, Lynch E, Sheffler W, Parry B, Jannetty N, Decarreau J, Wagenbach M, Vicente JJ, Chen J, Wang L, Dowling Q, Oberdorfer G, Stewart L, Wordeman L, De Yoreo J, Jacobs-Wagner C, Kollman J, Baker D.

Science. 2018 Nov 9;362(6415):705-709. doi: 10.1126/science.aau3775.

PMID:
30409885
2.

De novo design of a fluorescence-activating β-barrel.

Dou J, Vorobieva AA, Sheffler W, Doyle LA, Park H, Bick MJ, Mao B, Foight GW, Lee MY, Gagnon LA, Carter L, Sankaran B, Ovchinnikov S, Marcos E, Huang PS, Vaughan JC, Stoddard BL, Baker D.

Nature. 2018 Sep;561(7724):485-491. doi: 10.1038/s41586-018-0509-0. Epub 2018 Sep 12.

PMID:
30209393
3.

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
4.

Accurate computational design of multipass transmembrane proteins.

Lu P, Min D, DiMaio F, Wei KY, Vahey MD, Boyken SE, Chen Z, Fallas JA, Ueda G, Sheffler W, Mulligan VK, Xu W, Bowie JU, Baker D.

Science. 2018 Mar 2;359(6379):1042-1046. doi: 10.1126/science.aaq1739.

PMID:
29496880
5.

Confirmation of intersubunit connectivity and topology of designed protein complexes by native MS.

Sahasrabuddhe A, Hsia Y, Busch F, Sheffler W, King NP, Baker D, Wysocki VH.

Proc Natl Acad Sci U S A. 2018 Feb 6;115(6):1268-1273. doi: 10.1073/pnas.1713646115. Epub 2018 Jan 19.

6.

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site.

Strauch EM, Bernard SM, La D, Bohn AJ, Lee PS, Anderson CE, Nieusma T, Holstein CA, Garcia NK, Hooper KA, Ravichandran R, Nelson JW, Sheffler W, Bloom JD, Lee KK, Ward AB, Yager P, Fuller DH, Wilson IA, Baker D.

Nat Biotechnol. 2017 Jul;35(7):667-671. doi: 10.1038/nbt.3907. Epub 2017 Jun 12.

7.

Computational design of self-assembling cyclic protein homo-oligomers.

Fallas JA, Ueda G, Sheffler W, Nguyen V, McNamara DE, Sankaran B, Pereira JH, Parmeggiani F, Brunette TJ, Cascio D, Yeates TR, Zwart P, Baker D.

Nat Chem. 2017 Apr;9(4):353-360. doi: 10.1038/nchem.2673. Epub 2016 Dec 5.

8.

Computational design of a homotrimeric metalloprotein with a trisbipyridyl core.

Mills JH, Sheffler W, Ener ME, Almhjell PJ, Oberdorfer G, Pereira JH, Parmeggiani F, Sankaran B, Zwart PH, Baker D.

Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15012-15017. doi: 10.1073/pnas.1600188113. Epub 2016 Dec 8.

9.

Corrigendum: Design of a hyperstable 60-subunit protein icosahedron.

Hsia Y, Bale JB, Gonen S, Shi D, Sheffler W, Fong KK, Nattermann U, Xu C, Huang PS, Ravichandran R, Yi S, Davis TN, Gonen T, King NP, Baker D.

Nature. 2016 Dec 1;540(7631):150. doi: 10.1038/nature20108. Epub 2016 Oct 19. No abstract available.

PMID:
27760110
10.

Accurate design of megadalton-scale two-component icosahedral protein complexes.

Bale JB, Gonen S, Liu Y, Sheffler W, Ellis D, Thomas C, Cascio D, Yeates TO, Gonen T, King NP, Baker D.

Science. 2016 Jul 22;353(6297):389-94. doi: 10.1126/science.aaf8818.

11.

Design of a hyperstable 60-subunit protein dodecahedron. [corrected].

Hsia Y, Bale JB, Gonen S, Shi D, Sheffler W, Fong KK, Nattermann U, Xu C, Huang PS, Ravichandran R, Yi S, Davis TN, Gonen T, King NP, Baker D.

Nature. 2016 Jul 7;535(7610):136-9. doi: 10.1038/nature18010. Epub 2016 Jun 15. Erratum in: Nature. 2016 Dec 1;540(7631):150.

12.

Accurate design of co-assembling multi-component protein nanomaterials.

King NP, Bale JB, Sheffler W, McNamara DE, Gonen S, Gonen T, Yeates TO, Baker D.

Nature. 2014 Jun 5;510(7503):103-8. doi: 10.1038/nature13404. Epub 2014 May 25.

13.

Accelerated electron transport from photosystem I to redox partners by covalently linked ferredoxin.

Wittenberg G, Sheffler W, Darchi D, Baker D, Noy D.

Phys Chem Chem Phys. 2013 Dec 7;15(45):19608-14. doi: 10.1039/c3cp53264j. Epub 2013 Oct 16.

PMID:
24129892
14.

Computational design of self-assembling protein nanomaterials with atomic level accuracy.

King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, André I, Gonen T, Yeates TO, Baker D.

Science. 2012 Jun 1;336(6085):1171-4. doi: 10.1126/science.1219364.

15.

A new generation of crystallographic validation tools for the protein data bank.

Read RJ, Adams PD, Arendall WB 3rd, Brunger AT, Emsley P, Joosten RP, Kleywegt GJ, Krissinel EB, Lütteke T, Otwinowski Z, Perrakis A, Richardson JS, Sheffler WH, Smith JL, Tickle IJ, Vriend G, Zwart PH.

Structure. 2011 Oct 12;19(10):1395-412. doi: 10.1016/j.str.2011.08.006.

16.

Modeling disordered regions in proteins using Rosetta.

Wang RY, Han Y, Krassovsky K, Sheffler W, Tyka M, Baker D.

PLoS One. 2011;6(7):e22060. doi: 10.1371/journal.pone.0022060. Epub 2011 Jul 29.

17.

ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules.

Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, Ban YE, Fleishman SJ, Corn JE, Kim DE, Lyskov S, Berrondo M, Mentzer S, Popović Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P.

Methods Enzymol. 2011;487:545-74. doi: 10.1016/B978-0-12-381270-4.00019-6.

18.

RosettaHoles2: a volumetric packing measure for protein structure refinement and validation.

Sheffler W, Baker D.

Protein Sci. 2010 Oct;19(10):1991-5. doi: 10.1002/pro.458.

19.

Structure prediction for CASP8 with all-atom refinement using Rosetta.

Raman S, Vernon R, Thompson J, Tyka M, Sadreyev R, Pei J, Kim D, Kellogg E, DiMaio F, Lange O, Kinch L, Sheffler W, Kim BH, Das R, Grishin NV, Baker D.

Proteins. 2009;77 Suppl 9:89-99. doi: 10.1002/prot.22540.

20.
21.

Ranking predicted protein structures with support vector regression.

Qiu J, Sheffler W, Baker D, Noble WS.

Proteins. 2008 May 15;71(3):1175-82.

PMID:
18004754
22.

Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.

Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, Andre I, Baker D.

Proteins. 2007;69 Suppl 8:118-28.

PMID:
17894356
23.

A learned comparative expression measure for affymetrix genechip DNA microarrays.

Sheffler W, Upfal E, Sedivy J, Noble WS.

Proc IEEE Comput Syst Bioinform Conf. 2005:144-54.

PMID:
16447972
24.

Organisierter Massenmord an Juden in nationalsocialistischen Vernichtungslagern.

Arndt I, Sheffler W.

Vierteljahrsh Zeitgesch. 1976;24(2):105-35. German. No abstract available.

PMID:
11633496

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