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Items: 15

1.

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.

2.

Discovery of peptide ligands through docking and virtual screening at nicotinic acetylcholine receptor homology models.

Leffler AE, Kuryatov A, Zebroski HA, Powell SR, Filipenko P, Hussein AK, Gorson J, Heizmann A, Lyskov S, Tsien RW, Poget SF, Nicke A, Lindstrom J, Rudy B, Bonneau R, Holford M.

Proc Natl Acad Sci U S A. 2017 Sep 19;114(38):E8100-E8109. doi: 10.1073/pnas.1703952114. Epub 2017 Sep 5.

3.

Computing structure-based lipid accessibility of membrane proteins with mp_lipid_acc in RosettaMP.

Koehler Leman J, Lyskov S, Bonneau R.

BMC Bioinformatics. 2017 Feb 20;18(1):115. doi: 10.1186/s12859-017-1541-z.

4.

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.

5.

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.

6.

Peptiderive server: derive peptide inhibitors from protein-protein interactions.

Sedan Y, Marcu O, Lyskov S, Schueler-Furman O.

Nucleic Acids Res. 2016 Jul 8;44(W1):W536-41. doi: 10.1093/nar/gkw385. Epub 2016 May 3.

7.

DARC 2.0: Improved Docking and Virtual Screening at Protein Interaction Sites.

Gowthaman R, Lyskov S, Karanicolas J.

PLoS One. 2015 Jul 16;10(7):e0131612. doi: 10.1371/journal.pone.0131612. eCollection 2015.

8.

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.

9.

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.

10.

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.

11.

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.

12.

Real-time PyMOL visualization for Rosetta and PyRosetta.

Baugh EH, Lyskov S, Weitzner BD, Gray JJ.

PLoS One. 2011;6(8):e21931. doi: 10.1371/journal.pone.0021931. Epub 2011 Aug 16.

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.

PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta.

Chaudhury S, Lyskov S, Gray JJ.

Bioinformatics. 2010 Mar 1;26(5):689-91. doi: 10.1093/bioinformatics/btq007. Epub 2010 Jan 7.

15.

The RosettaDock server for local protein-protein docking.

Lyskov S, Gray JJ.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W233-8. doi: 10.1093/nar/gkn216. Epub 2008 Apr 28.

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