Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home

Proteins: Structure, Function and Genetics

Volumn 69, Issue SUPPL. 8, 2007, Pages 118-128

  Das, Rhiju ^a,b   Qian, Bin ^a   Raman, Srivatsan ^a,b   Vernon, Robert ^a   Thompson, James ^a,b   Bradley, Philip ^a   Khare, Sagar ^a   Tyka, Michael D ^a   Bhat, Divya ^a,b   Chivian, Dylan ^c   Kim, David E ^a   Sheffler, William H ^a,b   Malmström, Lars ^a   Wollacott, Andrew M ^a   Wang, Chu ^a   Andre, Ingemar ^a   Baker, David ^a,b  

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

^b UNIVERSITY OF WASHINGTON   (United States)

^c LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

All atom refinement; CASP; Fragment insertion; Free modeling; Protein structure prediction; Rosetta; Template based modeling

Indexed keywords

CASPASE 7;

COMPUTER NETWORK; COMPUTER PROGRAM; CONFERENCE PAPER; PREDICTION; PRIORITY JOURNAL; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; THERMODYNAMICS;

EID: 36749055649     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21636     Document Type: Conference Paper

References (32)

1. 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.
2. Bradley P, Misura KM, Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 2005;309:1868-1871.
3. Finn RD, Mistry J, Schuster-Bockler B, Griffiths-fones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A. Pfam: clans, web tools and services. Nucleic Acids Res 2006;34(Database issue):D247-D251.
4. Anderson DP. BOINC: A system for public-resource computing and storage, In 5th IEEE/ACM International Workshop on Grid Computing, Pittsburgh, USA, November 8, 2004.
5. Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics 2003;19:1015-1018.
6. Chivian D, Kim DE, Malmstrom L, Schonbrun J, Rohl CA, Baker D. Prediction of CASP6 structures using automated Roberta protocols. Proteins 2005;61(Suppl 7):157-166.
7. Kim DE, Chivian D, Malmstrom L, Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and Rosetta-DOM. Proteins 2005;61(Suppl 7):193-200.
8. Rohl CA, Strauss CE, Misura KM, Baker D. Protein structure prediction using Rosetta. Methods Enzymol 2004;383:66-93.
9. Schueler-Furman O, Wang C, Bradley P, Misura K, Baker D. Progress in modeling of protein structures and interactions. Science 2005;310:638-642.
10. Brooks BR, Bruccoleri RE, Olafson BD, States JD, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minmimization, and dynamics calculations. J Comp Chem 1983;4:187-217.
11. Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
12. Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acids Res 2003;31:3370-3374.
13. Plewczynski D, Pas J, Von Grotthuss M, Rychlewski L. Comparison of proteins based on segments structural similarity. Acta Biochim Pol 2004;51:161-172.
14. Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins 2004;55:656-677.
15. Canutescu AA, Dunbrack RL, Jr. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003;12:963-972.
16. Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci 2005;14:1328-1339.
17. Chivian D, Baker D. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic Acids Res 2006;34:e112.
18. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
19. Simons KT, Kooperberg C, Huang E, Baker D. Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 1997;268:209-225.
20. McGuffin LJ, Bryson K, Jones DT. The PSIPRED protein structure prediction server. Bioinformatics 2000;16:404-405.
21. Meiler J, Muller M, Zeidler A, Schmaschke F. Generation and evaluation of dimension reduced amino acid parameter representations by artificial neural networks. J Mol Model 2001;7:360-369.
22. Karplus K, Hu B. Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. Bioinformatics 2001;17:713-720.
23. Ouali M, King RD. Cascaded multiple classifiers for secondary structure prediction. Protein Sci 2000;9:1162-1176.
24. Bradley P, Baker D. Improved β-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 2006;65:922-929.
25. Eisenberg D, McLachlan AD. Solvation energy in protein folding and binding. Nature 1986;319:199-203.
26. Wollacott AM, Zanghellini A, Murphy P, Baker D. Prediction of structures of multidomain proteins from structures of the individual domains. Protein Sci 2007;16:165-175.
27. Berger B, Wilson DB, Wolf E, Tonchev T, Milla M, Kim PS. Predicting coiled coils by use of pairwise residue correlations. Proc Natl Acad Sci USA 1995;92:8259-8263.
28. Lupas A, Van Dyke M, Stock J. Predicting coiled coils from protein sequences. Science 1991;252:1162-1164.
29. 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.
30. Purushothaman SK, Bujnicki JM, Grosjean H, Lapeyre B. Trm11p and Trm112p are both required for the formation of 2-methylguanosine at position 10 in yeast tRNA. Mol Cell Biol 2005;25:4359-4370.
31. Zhang Y, Arakaki AK, Skolnick J. TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 2005;61(Suppl 7):91-98.
32. Meiler J, Baker D. Coupled prediction of protein secondary and tertiary structure. Proc Natl Acad Sci USA 2003;100:12105-12110.