Rosetta in CAPRI rounds 13-19

Proteins: Structure, Function and Bioinformatics

Volumn 78, Issue 15, 2010, Pages 3212-3218

  Fleishman, Sarel J ^a   Corn, Jacob E ^a   Strauch, Eva M ^a   Whitehead, Tim A ^a   Andre, Ingemar ^a   Thompson, James ^a,b   Havranek, James J ^c   Das, Rhiju ^d   Bradley, Philip ^e   Baker, David ^a,f  

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

^b UNIVERSITY OF WASHINGTON   (United States)

^c WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^d STANFORD UNIVERSITY   (United States)

^e Fred Hutchinson Cancer Research Center   (United States)

^f HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Backrub; CAPRI; Conformational changes; Docking; Flexible backbone modeling; Fragment insertion; Protein protein interactions; RNA protein interactions; Rosetta; Structure prediction

Indexed keywords

ARF PROTEIN;

ARTICLE; MOLECULAR DOCKING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RNA TRANSCRIPTION;

COMPUTATIONAL BIOLOGY; MODELS, CHEMICAL; MODELS, MOLECULAR; MONTE CARLO METHOD; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; RNA; RNA-BINDING PROTEINS; SOFTWARE;

EID: 77957943551     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22784     Document Type: Article

References (23)

1. Das R, Baker D. Macromolecular modeling with rosetta. Annu Rev Biochem 2008;77:363-382.
2. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
3. Kortemme T, Baker D. A simple physical model for binding energy hot spots in protein-protein complexes. Proc Natl Acad Sci USA 2002;99:14116-14121.
4. Tong Y, Chugha P, Hota PK, Alviani RS, Li M, Tempel W, Shen L, Park HW, Buck M. Binding of Rac1. Rnd1, and Rho D to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain. J Biol Chem 2007;282:37215-37224.
5. DeLano WL. The PyMol molecular graphics systems. Palo Alto, CA: DeLano Scientific, 2002.
6. Bradley P, Malmstrom L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KM, Baker D. Free modeling with Rosetta in CASP6. Proteins 2005;61(Suppl 7):128-134.
7. Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmstrom L, Wollacott AM, Wang C, Andre I, Baker D. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta @home. Proteins 2007;69(Suppl 8):118-128.
8. Schluckebier G, Zhong P, Stewart KD, Kavanaugh TJ, Abad-Zapatero C. The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogsimplications for the reaction mechanism. J Mol Biol 1999;289: 277-291.
9. Das R, Karanicolas J, Baker D. Atomic accuracy in predicting and designing noncanonical RNA structure. Nat Methods 2010;7:291294.
10. Douthwaite S, Jakobsen L, Yoshizawa S, Fourmy D. Interaction of the tylosin-resistance methyltransferase RlmA II at its rRNA target differs from the orthologue RlmA I. J Mol Biol 2008;378:969-975.
11. Das R, Andre I, Shen Y, Wu Y, Lemak A, Bansal S, Arrowsmith CH, Szyperski T, Baker D. Simultaneous prediction of protein folding and docking at high resolution. Proc Natl Acad Sci USA 2009;106:18978-18983.
12. Andre I, Bradley P, Wang C, Baker D. Prediction of the structure of symmetrical protein assemblies. Proc Natl Acad Sci USA 2007;104: 17656-17661.
13. O'Shea EK, Klemm JD, Kim PS, Alber T. X-ray structure of the GCN4 leucine zipper, a two-stranded, parallel coiled coil. Science 1991;254:539-544.
14. Isabet T, Montagnac G, Regazzoni K, Raynal B, El Khadali F, England P, Franco M, Chavrier P, Houdusse A, Menetrey J. The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4. EMBO J 2009;28:2835-2845.
15. Smith CA, Kortemme T. Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction. J Mol Biol 2008;380:742-756.
16. O'Neal CJ, Jobling MG, Holmes RK, Hol WG. Structural basis for the activation of cholera toxin by human ARF6-GTP. Science 2005;309:1093-1096.
17. Menetrey J, Perderiset M, Cicolari J, Dubois T, Elkhatib N, El Khadali F, Franco M, Chavrier P, Houdusse A. Structural basis for ARF1-mediated recruitment of ARHGAP21 to Golgi membranes. EMBO J 2007;26:1953-1962.
18. Vetter IR, Wittinghofer A. The guanine nucleotide-binding switch in three dimensions. Science 2001;294:1299-1304.
19. Soding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 2005;21:951-960.
20. Qian B, Raman S, Das R, Bradley P, McCoy AJ, Read RJ, Baker D. High-resolution structure prediction and the crystallographic phase problem. Nature 2007;450:259-264.
21. Katz BA, Finer-Moore J, Mortezaei R, Rich DH, Stroud RM. Episelection: novel Ki approximately nanomolar inhibitors of serine proteases selected by binding or chemistry on an enzyme surface. Biochemistry 1995;34:8264-8280.
22. Grzesiak A, Helland R, Smalas AO, Krowarsch D, Dadlez M, Otlewski J. Substitutions at the P(1) position in BPTI strongly affect the association energy with serine proteinases. J Mol Biol 2000;301:205-217.
23. Bao R, Zhou CZ, Jiang C, Lin SX, Chi CW, Chen Y. The ternary structure of the double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation. J Biol Chem 2009;284:26676-26684