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Items: 22

1.

High-precision automated reconstruction of neurons with flood-filling networks.

Januszewski M, Kornfeld J, Li PH, Pope A, Blakely T, Lindsey L, Maitin-Shepard J, Tyka M, Denk W, Jain V.

Nat Methods. 2018 Aug;15(8):605-610. doi: 10.1038/s41592-018-0049-4. Epub 2018 Jul 16.

PMID:
30013046
2.

Principles for computational design of binding antibodies.

Baran D, Pszolla MG, Lapidoth GD, Norn C, Dym O, Unger T, Albeck S, Tyka MD, Fleishman SJ.

Proc Natl Acad Sci U S A. 2017 Oct 10;114(41):10900-10905. doi: 10.1073/pnas.1707171114. Epub 2017 Sep 25.

3.

Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta.

O'Meara MJ, Leaver-Fay A, Tyka MD, Stein A, Houlihan K, DiMaio F, Bradley P, Kortemme T, Baker D, Snoeyink J, Kuhlman B.

J Chem Theory Comput. 2015 Feb 10;11(2):609-22. doi: 10.1021/ct500864r.

4.

AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.

Lapidoth GD, Baran D, Pszolla GM, Norn C, Alon A, Tyka MD, Fleishman SJ.

Proteins. 2015 Aug;83(8):1385-406. doi: 10.1002/prot.24779. Epub 2015 Jun 6.

5.

CXCL4-induced plaque macrophages can be specifically identified by co-expression of MMP7+S100A8+ in vitro and in vivo.

Erbel C, Tyka M, Helmes CM, Akhavanpoor M, Rupp G, Domschke G, Linden F, Wolf A, Doesch A, Lasitschka F, Katus HA, Gleissner CA.

Innate Immun. 2015 Apr;21(3):255-65. doi: 10.1177/1753425914526461. Epub 2014 Mar 24.

PMID:
24663337
6.

Relaxation of backbone bond geometry improves protein energy landscape modeling.

Conway P, Tyka MD, DiMaio F, Konerding DE, Baker D.

Protein Sci. 2014 Jan;23(1):47-55.

7.

An in vitro model to study heterogeneity of human macrophage differentiation and polarization.

Erbel C, Rupp G, Helmes CM, Tyka M, Linden F, Doesch AO, Katus HA, Gleissner CA.

J Vis Exp. 2013 Jun 12;(76):e50332. doi: 10.3791/50332.

8.

Scientific benchmarks for guiding macromolecular energy function improvement.

Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, Baker D, Kuhlman B.

Methods Enzymol. 2013;523:109-43. doi: 10.1016/B978-0-12-394292-0.00006-0.

9.

Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers.

Tyka MD, Jung K, Baker D.

J Comput Chem. 2012 Dec 5;33(31):2483-91. doi: 10.1002/jcc.23069. Epub 2012 Jul 27.

10.

Algorithm discovery by protein folding game players.

Khatib F, Cooper S, Tyka MD, Xu K, Makedon I, Popovic Z, Baker D, Players F.

Proc Natl Acad Sci U S A. 2011 Nov 22;108(47):18949-53. doi: 10.1073/pnas.1115898108. Epub 2011 Nov 7.

11.

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.

12.

Structure-guided forcefield optimization.

Song Y, Tyka M, Leaver-Fay A, Thompson J, Baker D.

Proteins. 2011 Jun;79(6):1898-909. doi: 10.1002/prot.23013. Epub 2011 Apr 12.

13.

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.

14.

Alternate states of proteins revealed by detailed energy landscape mapping.

Tyka MD, Keedy DA, André I, Dimaio F, Song Y, Richardson DC, Richardson JS, Baker D.

J Mol Biol. 2011 Jan 14;405(2):607-18. doi: 10.1016/j.jmb.2010.11.008. Epub 2010 Nov 10.

15.

NMR structure determination for larger proteins using backbone-only data.

Raman S, Lange OF, Rossi P, Tyka M, Wang X, Aramini J, Liu G, Ramelot TA, Eletsky A, Szyperski T, Kennedy MA, Prestegard J, Montelione GT, Baker D.

Science. 2010 Feb 19;327(5968):1014-8. doi: 10.1126/science.1183649. Epub 2010 Feb 4.

16.

Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry.

Wang C, Vernon R, Lange O, Tyka M, Baker D.

Protein Sci. 2010 Mar;19(3):494-506. doi: 10.1002/pro.327.

17.

Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8.

Krieger E, Joo K, Lee J, Lee J, Raman S, Thompson J, Tyka M, Baker D, Karplus K.

Proteins. 2009;77 Suppl 9:114-22. doi: 10.1002/prot.22570.

18.

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.

19.

Refinement of protein structures into low-resolution density maps using rosetta.

DiMaio F, Tyka MD, Baker ML, Chiu W, Baker D.

J Mol Biol. 2009 Sep 11;392(1):181-90. doi: 10.1016/j.jmb.2009.07.008. Epub 2009 Jul 8.

20.

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
21.

Absolute free-energy calculations of liquids using a harmonic reference state.

Tyka MD, Sessions RB, Clarke AR.

J Phys Chem B. 2007 Aug 16;111(32):9571-80. Epub 2007 Jul 26.

PMID:
17655215
22.

An efficient, path-independent method for free-energy calculations.

Tyka MD, Clarke AR, Sessions RB.

J Phys Chem B. 2006 Aug 31;110(34):17212-20.

PMID:
16928020

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