A fast method for large-scale de novo peptide and miniprotein structure prediction

Journal of Computational Chemistry

Volumn 31, Issue 4, 2010, Pages 726-738

  Maupetit, Julien ^a,b   Derreumaux, Philippe ^b   Tufféry, Pierre ^a  

^a INSERM   (France)

^b France   (France)

Author keywords

Coarse grained force field; Miniprotein; Peptide; Structural alphabet; Structure prediction

Indexed keywords

AMINO ACID SEQUENCE; BIOACTIVE PEPTIDES; COARSE-GRAINED; COARSE-GRAINED FORCE FIELD; COARSE-GRAINED FORCE FIELDS; ENERGY CONFORMATION; FAST METHODS; IN-SILICO; LARGE SCALE EXPERIMENTS; MINI-PROTEINS; NEW APPROACHES; RATIONAL DESIGN; RIGID CORE; ROOT-MEAN SQUARE DEVIATION; STILL MISSING; STRUCTURAL ALPHABET; STRUCTURE PREDICTION;

AMINO ACIDS; CALCIUM; CONFORMATIONS; HIDDEN MARKOV MODELS; NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; ORGANIC ACIDS; RESONANCE; RIGID STRUCTURES;

PEPTIDES;

PEPTIDE; PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; METHODOLOGY; MONTE CARLO METHOD; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PROBABILITY; PROTEIN CONFORMATION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; MAGNETIC RESONANCE SPECTROSCOPY; MARKOV CHAINS; MODELS, MOLECULAR; MONTE CARLO METHOD; PEPTIDES; PROTEIN CONFORMATION; PROTEINS;

EID: 76249128506     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21365     Document Type: Article

References (50)

1. Liu, F.; Baggerman, G.; Schoofs, L.; Wets, G. J Proteome Res 2008, 7, 4119.
2. Sang, Y.; Blecha, F. Anim Health Res Rev 2008, 9, 227.
3. Rogge, G.; Jones, D.; Hubert, G. W.; Lin, Y.; Kuhar, M. J. Nat Rev Neurosci 2008, 9, 747.
4. Hong, F.; Ming, L.; Yi, S.; Zhanxia, L.; Yongquan, W.; Chi, L. Peptides 2008, 29, 1062.
5. Erdmann, K.; Cheung, B. W. Y.; Schröder, H. J Nutr Biochem 2008, 19, 643.
6. Zellefrow, C. D.; Griffiths, J. S.; Saha, S.; Hodges, A. M.; Goodman, J. L.; Paulk, J.; Kritzer, J. A.; Schepartz, A. J Am Chem Soc 2006, 128, 16506.
7. Imperiali, B.; Ottesen, J. J. J Pept Res 1999, 54, 177.
8. Gellman, S. H.; Woolfson, D. N. Nat Struct Biol 2002, 9, 408.
9. Bradley, P.; Chivian, D.; Meiler, J.; Misura, K. M. S.; Rohl, C. A.;Schief, W. R.; Wedemeyer, W. J.; Schueler-Furman, O.; Murphy, P.; Schonbrun, J.; Strauss, C. E. M.; Baker, D. Proteins 2003, 53 (Suppl 6), 457.
10. Forcellino F.; Derreumaux, P. Proteins 2001, 45, 159.
11. Jang, S.; Shin, S.; Pak, Y. J Am Chem Soc 2002, 124, 4976.
12. Ulmschneider, J. P.; Jorgensen, W. L. J Am Chem Soc 2004, 126, 1849.
13. Clarke, O. J.; Parker, M. J. J Comput Chem 2008, 29, 1177.
14. Ho, B. K.; Dill, K. A. PLoS Comput Biol 2006, 2, e27.
15. Dinner, A. R.; Lazaridis, T.; Karplus, M. Proc Natl Acad Sci USA 1999, 96, 9068.
16. Fuchs, P. F. J.; Bonvin, A. M. J. J.; Bochicchio, B.; Pepe, A.; Alix, A. J. P.; Tamburro, A. M. Biophys J 2006, 90, 2745.
17. Chen, J.; Im, W., Brooks C. L. J Am Chem Soc 2006, 128, 3728.
18. Chebaro, Y.; Dong, X.; Laghaei, R.; Derreumaux, P.; Mousseau, N. J Phys Chem B 2009, 113, 267.
19. Ishikawa, K.; Yue, K.; Dill, K. A. Protein Sci 1999, 8, 716.
20. Kaur, H.; Garg, A.; Raghava, G. P. S. Protein Pept Lett 2007, 14, 626.
21. Thomas, A.; Deshayes, S.; Decaffmeyer, M.; Van Eyck, M. H.; Charloteaux, B.; Brasseur, R. Proteins 2006, 65, 889.
22. Nicosia, G.; Stracquadanio, G. Biophys J 2008, 95, 4988.
23. Camproux, A. C.; Tuffery, P.; Chevrolat, J. P.; Boisvieux, J. F.; Hazout, S. Protein Eng 1999, 12, 1063.
24. Camproux, A. C.; Gautier, R.; Tufféry, P. J Mol Biol 2004, 339, 591.
25. Tuffery, P.; Derreumaux, P. Proteins 2005, 61, 732.
26. Tuffery, P.; Guyon, F.; Derreumaux, P. J Comput Chem 2005, 26, 506.
27. Maupetit, J.; Tuffery, P.; Derreumaux, P. Proteins 2007, 69, 394.
28. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235.
29. Frishman, D.; Argos, P. Proteins 1995, 23, 566.
30. Jagielska, A.; Scheraga, H. A. J Comput Chem 2007, 28, 1068.
31. Yang, J. S.; Chen, W. W.; Skolnick, J.; Shakhnovich, E. I. Structure 2007, 15, 53.
32. Altschul, S. F.; Madden, T. L.; Schäffer, A. A.; Zhang, J.; Zhang, Z.; Miller, W.; Lipman, D. J. Nucleic Acids Res 1997, 25, 3389.
33. Suzek, B. E.; Huang, H.; McGarvey, P.; Mazumder, R.; Wu, C. H. Bioinformatics 2007, 23, 1282.
34. Derreumaux, P.; Mousseau, N. J Chem Phys 2007, 126, 025101.
35. Mousseau, N.; Derreumaux, P. Acc Chem Res 2005, 38, 885.
36. Song, W.; Wei, G.; Mousseau, N.; Derreumaux, P. J Phys Chem.B 2008, 112, 4410.
37. Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F.; Harano, Y.; Ioannidis, Y. E.; Lin, J.; Livny, M.; Mading, S.; Maziuk, D.; Miller, Z.; Nakatani, E.; Schulte, C. F.; Tolmie, D. E.; Kent Wenger, R.; Yao, H.; Markley, J. L. Nucleic Acids Res 2008, 36 (Database issue), D402.
38. Berjanskii, M. V.; Wishart, D. S. Nucleic Acids Res 2007, 35 (Web Server issue), W531.
39. Jones, D. T. J Mol Biol 1999, 292, 195.
40. Freddolino, P. L.; Liu, F.; Gruebele, M.; Schulten, K. Biophys J 2008, 94, L75.
41. Casarotto, M. G.; Gibson, F.; Pace, S. M.; Curtis, S. M.; Mulcair, M.; Dulhunty, A. F. J Biol Chem 2000, 275, 11631.
42. Siedlecka, M.; Goch, G.; Ejchart, A.; Sticht, H.; Bierzynski, A. Proc Natl Acad Sci USA 1999, 96, 903.
43. Rozek, A.; Friedrich, C. L.; Hancock, R. E. Biochemistry 2000, 39, 15765.
44. Tinoco, L. W. Da Silva, A.; Leite, A.; Valente, A. P.; Almeida, F. C. L. J Biol Chem 2002, 277, 36351.
45. Pitera, J. W. Swope, W. Proc Natl Acad Sci USA 2003, 100, 7587.
46. Kannan, S.; Zacharias, M. Proteins 2007, 66, 697.
47. Duan, Y.; Kollman, P. A. Science 1998, 282, 740.
48. Lei, H.; Deng, X.; Wang, Z.; Duan, Y. J Chem Phys 2008, 129, 155104.
49. Verma, A.; Gopal, S. M.; Oh, J. S.; Lee, K. H.; Wenzel, W. J Comput Chem 2007, 28, 2552.
50. Ding, F.; Tsao, D.; Nie, H.; Dokholyan, N. V. Structure 2008, 16, 1010.