Rosettascripts: A scripting language interface to the Rosetta Macromolecular modeling suite

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Fleishman, Sarel J ^a   Leaver Fay, Andrew ^b   Corn, Jacob E ^a,e   Strauch, Eva Maria ^a   Khare, Sagar D ^a   Koga, Nobuyasu ^a   Ashworth, Justin ^a,f   Murphy, Paul ^a   Richter, Florian ^a   Lemmon, Gordon ^c   Meiler, Jens ^c   Baker, David ^a,d  

^a UNIVERSITY OF WASHINGTON SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^c VANDERBILT UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d UNIVERSITY OF WASHINGTON   (United States)

^e GENENTECH INC   (United States)

^f INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; DNA BINDING PROTEIN; LIGAND;

ARTICLE; COMMUNICATION PROTOCOL; COMPUTER INTERFACE; COMPUTER LANGUAGE; COMPUTER SECURITY; DATA ANALYSIS; DATA ANALYSIS SOFTWARE; HUMAN COMPUTER INTERACTION; MACROMOLECULAR MODELING; MACROMOLECULE; MOLECULAR DOCKING; MOLECULAR MODEL; PROTEIN STABILITY; SEQUENCE ANALYSIS; WEB BROWSER; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; PROTEIN CONFORMATION;

DNA-BINDING PROTEINS; LIGANDS; MODELS, MOLECULAR; PROGRAMMING LANGUAGES; PROTEIN CONFORMATION; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 79959615159     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020161     Document Type: Article

References (30)

1. Kuhlman B, Baker D, (2000) Native protein sequences are close to optimal for their structures. Proc Natl Acad Sci USA 97: 10383-10388.
2. Kuhlman B, Dantas G, Ireton GC, Varani G, Stoddard BL, et al. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302: 1364-1368.
3. Korkegian A, Black ME, Baker D, Stoddard BL, (2005) Computational thermostabilization of an enzyme. Science 308: 857-860.
4. Rothlisberger D, Khersonsky O, Wollacott AM, Jiang L, DeChancie J, et al. (2008) Kemp elimination catalysts by computational enzyme design. Nature 453: 190-195.
5. Jiang L, Althoff EA, Clemente FR, Doyle L, Rothlisberger D, et al. (2008) De novo computational design of retro-aldol enzymes. Science 319: 1387-1391.
6. Fleishman SJ, Whitehead TA, Ekiert DC, Dreyfus C, Corn JE, et al. (2011) Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 332: 816-821.
7. Kortemme T, Joachimiak LA, Bullock AN, Schuler AD, Stoddard BL, et al. (2004) Computational redesign of protein-protein interaction specificity. Nat Struct Mol Biol 11: 371-379.
8. Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ Jr, et al. (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature 441: 656-659.
9. Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, et al. (2010) Rosetta3 an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol 487: 545-574.
10. Meyers S, (2005) Effective C++. Boston Addison-Wesley.
11. Chaudhury S, Lyskov S, Gray JJ, (2010) PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta. Bioinformatics 26: 689-691.
12. Lee B, Richards FM, (1971) The interpretation of protein structures: estimation of static accessibility. J Mol Biol 55: 379-400.
13. Sandberg WS, Terwilliger TC, (1989) Influence of interior packing and hydrophobicity on the stability of a protein. Science 245: 54-57.
14. Sheffler W, Baker D, (2009) RosettaHoles: rapid assessment of protein core packing for structure prediction, refinement, design, and validation. Protein Sci 18: 229-239.
15. Tyka MD, Keedy DA, Andre I, Dimaio F, Song Y, et al. (2010) Alternate States of proteins revealed by detailed energy landscape mapping. J Mol Biol 405: 607-618.
16. Lerner RA, (2006) Manufacturing immunity to disease in a test tube: the magic bullet realized. Angew Chem Int Ed Engl 45: 8106-8125.
17. Leaver-Fay A, Kuhlman B, Snoeyink J, (2005) An adaptive dynamic programming algorithm for the side chain placement problem. Pac Symp Biocomput pp. 16-27.
18. Guntas G, Purbeck C, Kuhlman B, (2010) Engineering a protein-protein interface using a computationally designed library. Proc Natl Acad Sci U S A 107: 19296-19301.
19. Smith CA, Kortemme T, (2008) Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. Jô Mol Biol 380: 742-756.
20. Davis IW, Arendall WB 3rd, Richardson DC, Richardson JS, (2006) The backrub motion: how protein backbone shrugs when a sidechain dances. Structure 14: 265-274.
21. Das R, Baker D, (2008) Macromolecular modeling with rosetta. Annu Rev Biochem 77: 363-382.
22. Canutescu AA, Dunbrack RL Jr, (2003) Cyclic coordinate descent: A robotics algorithm for protein loop closure. Prot Sci 12: 963-972.
23. Mandell DJ, Coutsias EA, Kortemme T, (2009) Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nat Methods 6: 551-552.
24. Zanghellini A, Jiang L, Wollacott AM, Cheng G, Meiler J, et al. (2006) New algorithms and an in silico benchmark for computational enzyme design. Protein Sci 15: 2785-2794.
25. Meiler J, Baker D, (2006) ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65: 538-548.
26. Davis IW, Baker D, (2009) RosettaLigand docking with full ligand and receptor flexibility. Jô Mol Biol 385: 381-392.
27. Havranek JJ, Duarte CM, Baker D, (2004) A simple physical model for the prediction and design of protein-DNA interactions. Jô Mol Biol 344: 59-70.
28. Ashworth J, Taylor GK, Havranek JJ, Quadri SA, Stoddard BL, et al. (2010) Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs. Nucleic Acids Res 38: 5601-5608.
29. Thyme SB, Jarjour J, Takeuchi R, Havranek JJ, Ashworth J, et al. (2009) Exploitation of binding energy for catalysis and design. Nature 461: 1300-1304.
30. Havranek JJ, Baker D, (2009) Motif-directed flexible backbone design of functional interactions. Protein Sci 18: 1293-1305.