Improvements to Robotics-Inspired Conformational Sampling in Rosetta

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Stein, Amelie ^a   Kortemme, Tanja ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ACCURACY; ARTICLE; CONFORMATION; KINEMATICS; MOLECULAR BIOLOGY; MOLECULAR MODEL; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; ROBOTICS; SAMPLING;

ALGORITHMS; BIOMECHANICAL PHENOMENA; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; ROBOTICS; THERMODYNAMICS;

EID: 84878000040     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0063090     Document Type: Article

References (49)

1. Fleishman SJ, Baker D, (2012) Role of the biomolecular energy gap in protein design, structure, and evolution. Cell 149: 262-273.
2. Sohl JL, Jaswal SS, Agard DA, (1998) Unfolded conformations of alpha-lytic protease are more stable than its native state. Nature 395: 817-819.
3. Das R, (2011) Four Small Puzzles That Rosetta Doesn't Solve. PLoS ONE 6: e20044.
4. Mandell DJ, Coutsias EA, Kortemme T, (2009) Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nature methods 6: 551-552.
5. Bradley P, Misura KM, Baker D, (2005) Toward high-resolution de novo structure prediction for small proteins. Science 309: 1868-1871.
6. Qian B, Raman S, Das R, Bradley P, McCoy AJ, et al. (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450: 259-264.
7. Lange OF, Baker D, (2012) Resolution-adapted recombination of structural features significantly improves sampling in restraint-guided structure calculation. Proteins 80: 884-895.
8. Das R, Baker D, (2008) Macromolecular modeling with rosetta. Annual review of biochemistry 77: 363-382.
9. Raman S, Lange OF, Rossi P, Tyka M, Wang X, et al. (2010) NMR structure determination for larger proteins using backbone-only data. Science 327: 1014-1018.
10. Liwo A, Czaplewski C, Oldziej S, Scheraga HA, (2008) Computational techniques for efficient conformational sampling of proteins. Current opinion in structural biology 18: 134-139.
11. Simons KT, Kooperberg C, Huang E, Baker D, (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. Journal of molecular biology 268: 209-225.
12. Kirkpatrick S, Gelatt CD Jr, Vecchi MP, (1983) Optimization by simulated annealing. Science 220: 671-680.
13. Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, et al. (2011) ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in enzymology 487: 545-574.
14. Murphy PM, Bolduc JM, Gallaher JL, Stoddard BL, Baker D, (2009) Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences of the United States of America 106: 9215-9220.
15. Hu X, Wang H, Ke H, Kuhlman B, (2007) High-resolution design of a protein loop. Proceedings of the National Academy of Sciences of the United States of America 104: 17668-17673.
16. Huang PS, Ban YE, Richter F, Andre I, Vernon R, et al. (2011) RosettaRemodel: a generalized framework for flexible backbone protein design. PLoS ONE 6: e24109.
17. Koga N, Tatsumi-Koga R, Liu G, Xiao R, Acton TB, et al. (2012) Principles for designing ideal protein structures. Nature 491: 222-227.
18. Azoitei ML, Correia BE, Ban YE, Carrico C, Kalyuzhniy O, et al. (2011) Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science 334: 373-376.
19. Sellers BD, Zhu K, Zhao S, Friesner RA, Jacobson MP, (2008) Toward better refinement of comparative models: predicting loops in inexact environments. Proteins 72: 959-971.
20. Wang C, Bradley P, Baker D, (2007) Protein-protein docking with backbone flexibility. Journal of molecular biology 373: 503-519.
21. Felts AK, Gallicchio E, Chekmarev D, Paris KA, Friesner RA, et al. (2008) Prediction of Protein Loop Conformations using the AGBNP Implicit Solvent Model and Torsion Angle Sampling. Journal of chemical theory and computation 4: 855-868.
22. Kim DE, Blum B, Bradley P, Baker D, (2009) Sampling bottlenecks in de novo protein structure prediction. Journal of molecular biology 393: 249-260.
23. Berkholz DS, Driggers CM, Shapovalov MV, Dunbrack RL Jr, Karplus PA, (2012) Nonplanar peptide bonds in proteins are common and conserved but not biased toward active sites. Proceedings of the National Academy of Sciences of the United States of America 109: 449-453.
24. Ting D, Wang G, Shapovalov M, Mitra R, Jordan MI, et al. (2010) Neighbor-dependent Ramachandran probability distributions of amino acids developed from a hierarchical Dirichlet process model. PLoS computational biology 6: e1000763.
25. Shortle D, Simons KT, Baker D, (1998) Clustering of low-energy conformations near the native structures of small proteins. Proceedings of the National Academy of Sciences of the United States of America 95: 11158-11162.
26. Kapp GT, Liu S, Stein A, Wong DT, Remenyi A, et al. (2012) Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair. Proceedings of the National Academy of Sciences of the United States of America 109: 5277-5282.
27. Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, et al. (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of molecular biology 331: 281-299.
28. Misura KM, Baker D, (2005) Progress and challenges in high-resolution refinement of protein structure models. Proteins 59: 15-29.
29. Raveh B, London N, Schueler-Furman O, (2010) Sub-angstrom modeling of complexes between flexible peptides and globular proteins. Proteins 78: 2029-2040.
30. Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta crystallographica Section D, Biological crystallography 66: 12-21.
31. Boomsma W, Hamelryck T, (2005) Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space. BMC bioinformatics 6: 159.
32. Bruccoleri R, Karplus M, (1985) Chain closure with bond angle variations. Macromolecules 18: 2767-2773.
33. Ulmschneider JP, Jorgensen WL, (2003) Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias. The Journal of chemical physics 118: 4261-4271.
34. Canutescu AA, Dunbrack RL, (2003) Cyclic coordinate descent: A robotics algorithm for protein loop closure. Protein science: a publication of the Protein Society 12: 963-972.
35. Gront D, Kulp DW, Vernon RM, Strauss CE, Baker D, (2011) Generalized fragment picking in Rosetta: design, protocols and applications. PLoS ONE 6: e23294.
36. Tyka MD, Jung K, Baker D, (2012) Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. Journal of computational chemistry 33: 2483-2491.
37. Mandell DJ, Kortemme T, (2009) Backbone flexibility in computational protein design. Current opinion in biotechnology 20: 420-428.
38. Richter F, Leaver-Fay A, Khare SD, Bjelic S, Baker D, (2011) De novo enzyme design using Rosetta3. PLoS ONE 6: e19230.
39. Richter F, Blomberg R, Khare SD, Kiss G, Kuzin AP, et al. (2012) Computational design of catalytic dyads and oxyanion holes for ester hydrolysis. Journal of the American Chemical Society 134: 16197-16206.
40. Lee J, Lee D, Park H, Coutsias EA, Seok C, (2010) Protein loop modeling by using fragment assembly and analytical loop closure. Proteins 78: 3428-3436.
41. Liwo A, Lee J, Ripoll DR, Pillardy J, Scheraga HA, (1999) Protein structure prediction by global optimization of a potential energy function. Proceedings of the National Academy of Sciences of the United States of America 96: 5482-5485.
42. Lee J, Scheraga HA, Rackovsky S, (1997) New optimization method for conformational energy calculations on polypeptides: conformational space annealing. Journal of computational chemistry 18: 1222-1232.
43. Zhao S, Zhu K, Li J, Friesner RA, (2011) Progress in super long loop prediction. Proteins 79: 2920-2935.
44. Bower MJ, Cohen FE, Dunbrack RL, (1997) Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. Journal of molecular biology 267: 1268-1282.
45. Dunbrack RL, (2002) Rotamer libraries in the 21st century. Current opinion in structural biology 12: 431-440.
46. Dunbrack RL, Cohen FE, (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein science: a publication of the Protein Society 6: 1661-1681.
47. Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, et al. (2013) Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement. Methods in Enzymology 523.
48. Fleishman SJ, Leaver-Fay A, Corn JE, Strauch EM, Khare SD, et al. (2011) RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite. PLoS ONE 6: e20161.
49. Schrodinger LLC (2010) The PyMOL Molecular Graphics System, Version 1.3r1.