BCL::Score-Knowledge Based Energy Potentials for Ranking Protein Models Represented by Idealized Secondary Structure Elements

PLoS ONE

Volumn 7, Issue 11, 2012, Pages

  Woetzel, Nils ^a   Karakaş, Mert ^a   Staritzbichler, Rene ^a   Müller, Ralf ^a   Weiner, Brian E ^a   Meiler, Jens ^a  

^a VANDERBILT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; CRYSTAL STRUCTURE; ELECTRON SPIN RESONANCE; HYDROPHOBICITY; MATHEMATICAL ANALYSIS; NUCLEAR MAGNETIC RESONANCE; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN DATABASE; PROTEIN DOMAIN; PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; SMALL ANGLE SCATTERING; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; BAYES THEOREM; COMPUTATIONAL BIOLOGY; MODELS, MOLECULAR; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; ROTATION; THERMODYNAMICS;

EID: 84869223129     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049242     Document Type: Article

References (48)

1. Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, et al. (1958) A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181: 662-666.
2. Wüthrich K, (1990) Protein structure determination in solution by NMR spectroscopy. The Journal of biological chemistry 265: 22059-22062.
3. Berman HM, (2008) The Protein Data Bank: a historical perspective. Acta crystallographica Section A, Foundations of crystallography 64: 88-95.
4. Loll P, (2003) Membrane protein structural biology: the high throughput challenge. Journal of Structural Biology 142: 144-153.
5. Alber F, Dokudovskaya S, Veenhoff LM, Zhang W, Kipper J, et al. (2007) Determining the architectures of macromolecular assemblies. Nature 450: 683-694.
6. Lepault J, Booy FP, Dubochet J, (1983) Electron microscopy of frozen biological suspensions. Journal of microscopy 129: 89-102.
7. Saban SD, Silvestry M, Nemerow GR, Stewart PL, (2006) Visualization of alpha-helices in a 6-angstrom resolution cryoelectron microscopy structure of adenovirus allows refinement of capsid protein assignments. Journal of virology 80: 12049-12059.
8. Lindert S, Stewart PL, Meiler J, (2009) Hybrid approaches: applying computational methods in cryo-electron microscopy. Current opinion in structural biology 19: 218-225.
9. Lindert S, Staritzbichler R, Wötzel N, Karakaş M, Stewart PL, et al. (2009) EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps. Structure (London, England?: 1993) 17: 990-1003.
10. Svergun DI, (2010) Small-angle X-ray and neutron scattering as a tool for structural systems biology. Biological chemistry 391: 737-743.
11. Alexander N, Bortolus M, Al-Mestarihi A, Mchaourab H, Meiler J, (2008) De novo high-resolution protein structure determination from sparse spin-labeling EPR data. Structure (London, England?: 1993) 16: 181-195.
12. Van Eps N, Preininger AM, Alexander N, Kaya AI, Meier S, et al. (2011) Interaction of a G protein with an activated receptor opens the interdomain interface in the alpha subunit. Proceedings of the National Academy of Sciences of the United States of America 108: 9420-9424.
13. Kalkhof S, Haehn S, Paulsson M, Smyth N, Meiler J, et al. (2010) Computational modeling of laminin N-terminal domains using sparse distance constraints from disulfide bonds and chemical cross-linking. Proteins 78: 3409-3427.
14. Anfinsen CB, (1972) The formation and stabilization of protein structure. The Biochemical journal 128: 737-749.
15. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, et al. (1983) CHARMM- A PROGRAM FOR MACROMOLECULAR ENERGY, MINIMIZATION, AND DYNAMICS CALCULATIONS. Journal of Computational Chemistry 4: 187-217.
16. Ponder JW, Case DA (2003) Force fields for protein simulations Vol. 66. p. 27-+.
17. Novotný J, Bruccoleri R, Karplus M, (1984) An analysis of incorrectly folded protein models. Implications for structure predictions. Journal of molecular biology 177: 787-818.
18. Miyazawa S, Jernigan RL, (1985) Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules 18: 534-552.
19. Jones DT, Taylor WR, Thornton JM, (1992) A new approach to protein fold recognition. Nature 358: 86-89.
20. Shen M-Y, Sali A, (2006) Statistical potential for assessment and prediction of protein structures. Protein science?: a publication of the Protein Society 15: 2507-2524.
21. 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.
22. Sippl MJ, (1990) Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins. Journal of molecular biology 213: 859-883.
23. Hamelryck T, Borg M, Paluszewski M, Paulsen J, Frellsen J, et al. (2010) Potentials of mean force for protein structure prediction vindicated, formalized and generalized. PloS one 5: e13714.
24. John B, Sali A, (2003) Comparative protein structure modeling by iterative alignment, model building and model assessment. Nucleic acids research 31: 3982-3992.
25. Simons KT, Fox BA, Ruczinski I, Kooperberg C, Bystroff C, et al. (1999) Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. Proteins 34: 82-95.
26. 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.
27. Rohl CA, Strauss CEM, Chivian D, Baker D, (2004) Modeling structurally variable regions in homologous proteins with rosetta. Proteins 55: 656-677.
28. Mandell DJ, Coutsias EA, Kortemme T, (2009) Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. Nature methods 6: 551-552.
29. Krivov GG, Shapovalov MV, Dunbrack RL, (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins 77: 778-795.
30. Kaufmann KW, Lemmon GH, Deluca SL, Sheehan JH, Meiler J, (2010) Practically useful: what the Rosetta protein modeling suite can do for you. Biochemistry 49: 2987-2998.
31. Durham E, Dorr B, Woetzel N, Staritzbichler R, Meiler J, (2009) Solvent accessible surface area approximations for rapid and accurate protein structure prediction. Journal of molecular modeling 15: 1093-1108.
32. Hsin J, Arkhipov A, Yin Y, Stone JE, Schulten K (2008) Using VMD: an introductory tutorial. Current protocols in bioinformatics/ editoral board, Andreas D Baxevanis [et al] Chapter 5: Unit 5.7.
33. Ivankov DN, Garbuzynskiy SO, Alm E, Plaxco KW, Baker D, et al. (2003) Contact order revisited: influence of protein size on the folding rate. Protein science?: a publication of the Protein Society 12: 2057-2062.
34. Flory P (1953) Principles of Polymer Chemistry. Cornell University Press. p.
35. Meiler J, Zeidler A, Schmaeschke F, Mueller M, (2001) Generation and evaluation of dimension-reduced amino acid parameter representations by artificial neural networks. Journal of Molecular Modeling 7: 360-369.
36. Jones DT, (1999) Protein secondary structure prediction based on position-specific scoring matrices. Journal of molecular biology 292: 195-202.
37. Carugo O, Pongor S, (2001) A normalized root-mean-square distance for comparing protein three-dimensional structures. Protein science?: a publication of the Protein Society 10: 1470-1473.
38. Zemla a, Venclovas C, Moult J, Fidelis K (1999) Processing and analysis of CASP3 protein structure predictions. Proteins Suppl 3: 22-29.
39. Samudrala R, Levitt M, (2000) Decoys "R" Us: a database of incorrect conformations to improve protein structure prediction. Protein science?: a publication of the Protein Society 9: 1399-1401.
40. Frank J, (2009) Single-particle reconstruction of biological macromolecules in electron microscopy-30 years. Quarterly reviews of biophysics 42: 139-158.
41. Klug CS, Feix JB, (2008) Methods and applications of site-directed spin labeling EPR spectroscopy. Methods in cell biology 84: 617-658.
42. Wang G, Dunbrack RL, (2005) PISCES: recent improvements to a PDB sequence culling server. Nucleic acids research 33: W94-8.
43. Andreeva A, Howorth D, Chandonia J-M, Brenner SE, Hubbard TJP, et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic acids research 36: D419-25.
44. Cuff AL, Sillitoe I, Lewis T, Clegg AB, Rentzsch R, et al. (2011) Extending CATH: increasing coverage of the protein structure universe and linking structure with function. Nucleic acids research 39: D420-6.
45. 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.
46. Kabsch W, Sander C, (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22: 2577-2637.
47. Metropolis N, Ulam S, (1949) The Monte Carlo method. Journal of the American Statistical Association 44: 335-341.
48. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E, (1953) Equation of State Calculations by Fast Computing Machines. The Journal of Chemical Physics 21: 1087.