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Items: 20

1.

Genetic circuit characterization and debugging using RNA-seq.

Gorochowski TE, Espah Borujeni A, Park Y, Nielsen AA, Zhang J, Der BS, Gordon DB, Voigt CA.

Mol Syst Biol. 2017 Nov 9;13(11):952. doi: 10.15252/msb.20167461.

2.

DNAplotlib: Programmable Visualization of Genetic Designs and Associated Data.

Der BS, Glassey E, Bartley BA, Enghuus C, Goodman DB, Gordon DB, Voigt CA, Gorochowski TE.

ACS Synth Biol. 2017 Jul 21;6(7):1115-1119. doi: 10.1021/acssynbio.6b00252. Epub 2016 Oct 27.

PMID:
27744689
3.

Probing the minimal determinants of zinc binding with computational protein design.

Guffy SL, Der BS, Kuhlman B.

Protein Eng Des Sel. 2016 Aug;29(8):327-338. doi: 10.1093/protein/gzw026. Epub 2016 Jun 29.

4.

Genetic circuit design automation.

Nielsen AA, Der BS, Shin J, Vaidyanathan P, Paralanov V, Strychalski EA, Ross D, Densmore D, Voigt CA.

Science. 2016 Apr 1;352(6281):aac7341. doi: 10.1126/science.aac7341.

5.

Computational de novo design of a four-helix bundle protein--DND_4HB.

Murphy GS, Sathyamoorthy B, Der BS, Machius MC, Pulavarti SV, Szyperski T, Kuhlman B.

Protein Sci. 2015 Apr;24(4):434-45. doi: 10.1002/pro.2577. Epub 2014 Nov 6.

6.

Cages from coils.

Der BS, Kuhlman B.

Nat Biotechnol. 2013 Sep;31(9):809-10. doi: 10.1038/nbt.2670. No abstract available.

PMID:
24022157
7.

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.

8.

Strategies to control the binding mode of de novo designed protein interactions.

Der BS, Kuhlman B.

Curr Opin Struct Biol. 2013 Aug;23(4):639-46. doi: 10.1016/j.sbi.2013.04.010. Epub 2013 May 31. Review.

9.

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.

10.

Combined computational design of a zinc-binding site and a protein-protein interaction: one open zinc coordination site was not a robust hotspot for de novo ubiquitin binding.

Der BS, Jha RK, Lewis SM, Thompson PM, Guntas G, Kuhlman B.

Proteins. 2013 Jul;81(7):1245-55. doi: 10.1002/prot.24280. Epub 2013 Apr 20. Erratum in: Proteins. 2013 Sep;81(9):1678. Jha, Raamesh K [corrected to Jha, Ramesh K].

11.

Structure-based design of supercharged, highly thermoresistant antibodies.

Miklos AE, Kluwe C, Der BS, Pai S, Sircar A, Hughes RA, Berrondo M, Xu J, Codrea V, Buckley PE, Calm AM, Welsh HS, Warner CR, Zacharko MA, Carney JP, Gray JJ, Georgiou G, Kuhlman B, Ellington AD.

Chem Biol. 2012 Apr 20;19(4):449-55. doi: 10.1016/j.chembiol.2012.01.018.

12.

Catalysis by a de novo zinc-mediated protein interface: implications for natural enzyme evolution and rational enzyme engineering.

Der BS, Edwards DR, Kuhlman B.

Biochemistry. 2012 May 8;51(18):3933-40. doi: 10.1021/bi201881p. Epub 2012 Apr 24.

13.

Crystallization and preliminary X-ray crystallographic analysis of ligand-free and arginine-bound forms of Thermotoga maritima arginine-binding protein.

Ruggiero A, Dattelbaum JD, Pennacchio A, Iozzino L, Staiano M, Luchansky MS, Der BS, Berisio R, D'Auria S, Vitagliano L.

Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Nov 1;67(Pt 11):1462-5. doi: 10.1107/S1744309111037341. Epub 2011 Oct 27.

14.

Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer.

Der BS, Machius M, Miley MJ, Mills JL, Szyperski T, Kuhlman B.

J Am Chem Soc. 2012 Jan 11;134(1):375-85. doi: 10.1021/ja208015j. Epub 2011 Dec 15.

15.

Biochemistry. From computational design to a protein that binds.

Der BS, Kuhlman B.

Science. 2011 May 13;332(6031):801-2. doi: 10.1126/science.1207082. No abstract available.

PMID:
21566181
16.

Design of active transport must be highly intricate: a possible role of myosin and Ena/VASP for G-actin transport in filopodia.

Zhuravlev PI, Der BS, Papoian GA.

Biophys J. 2010 Apr 21;98(8):1439-48. doi: 10.1016/j.bpj.2009.12.4325.

17.

Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima. 2. Molecular organization and structural stability.

Scirè A, Marabotti A, Staiano M, Iozzino L, Luchansky MS, Der BS, Dattelbaum JD, Tanfani F, D'Auria S.

Mol Biosyst. 2010 Apr;6(4):687-98. doi: 10.1039/b922092e. Epub 2010 Feb 22.

PMID:
20237647
18.

Amino acid transport in thermophiles: characterization of an arginine-binding protein in Thermotoga maritima.

Luchansky MS, Der BS, D'Auria S, Pocsfalvi G, Iozzino L, Marasco D, Dattelbaum JD.

Mol Biosyst. 2010 Jan;6(1):142-51. doi: 10.1039/b908412f. Epub 2009 Sep 22.

PMID:
20024076
19.

Construction of a reagentless glucose biosensor using molecular exciton luminescence.

Der BS, Dattelbaum JD.

Anal Biochem. 2008 Apr 1;375(1):132-40. Epub 2007 Nov 17.

PMID:
18082614
20.

Analysis of ligand binding to a ribose biosensor using site-directed mutagenesis and fluorescence spectroscopy.

Vercillo NC, Herald KJ, Fox JM, Der BS, Dattelbaum JD.

Protein Sci. 2007 Mar;16(3):362-8. Epub 2007 Jan 22.

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