The long coming of computational structural biology

Journal of Structural Biology

Volumn 163, Issue 3, 2008, Pages 254-257

  Lupas, Andrei N ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

Author keywords

CASP; Computational structural biology; Modeling; Protein folding problem; Structure prediction

Indexed keywords

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; COMPUTER PROGRAM; CRYSTAL STRUCTURE; MATHEMATICAL COMPUTING; MOLECULAR BIOLOGY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; PROTEIN STRUCTURE;

COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; HISTORY, 20TH CENTURY; HISTORY, 21ST CENTURY; MOLECULAR CONFORMATION; PROTEIN FOLDING;

EID: 51349117730     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2008.02.006     Document Type: Article

References (67)

1. Aertgeerts K., De Ranter C.J., Booth N.A., and Declerck P.J. Rational design of complex formation between plasminogen activator inhibitor-1 and its target proteinases. J. Struct. Biol. 118 (1997) 236-242
2. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 215 (1990) 403-410
3. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
4. Ammelburg M., Frickey T., and Lupas A.N. Classification of AAA+ proteins. J. Struct. Biol. 156 (2006) 2-11
5. Andrade M.A., Perez-Iratxeta C., and Ponting C.P. Protein repeats: structures, functions, and evolution. J. Struct. Biol. 134 (2001) 117-131
6. Anfinsen C.B., Haber E., Sela M., and White Jr. F.H. The kinetics of formation of native ribonuclease during oxidation of the reduced polypeptide chain. Proc. Natl. Acad. Sci. USA 47 (1961) 1309-1314
7. Aydt E.M., Wolff G., and Morano I. Molecular modeling of the myosin-S1(A1) isoform. J. Struct. Biol. 159 (2007) 158-163
8. Borrell B. Power play. Nature 451 (2008) 240-243
9. Bradley P., Misura K.M., and Baker D. Toward high-resolution de novo structure prediction for small proteins. Science 309 (2005) 1868-1871
10. Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., and Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4 (1983) 187-217
11. Crick F.H.C. Is α-keratin a coiled coil?. Nature 170 (1952) 882-883
12. Crick F.H.C. The Fourier transform of a coiled-coil. Acta Cryst. 6 (1953) 685-689
13. Crick F.H.C. The packing of α-helices: simple coiled-coils. Acta Cryst. 6 (1953) 689-697
14. + channels in open, closed, and inactivated conformations. J. Struct. Biol. 121 (1998) 263-284
15. Eddy S.R. Profile hidden Markov models. Bioinformatics 14 (1998) 755-763
16. Ensign D.L., Kasson P.M., and Pande V.S. Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. J. Mol. Biol. 374 (2007) 806-816
17. Frickey T., and Lupas A.N. Phylogenetic analysis of AAA proteins. J. Struct. Biol. 146 (2004) 2-10
18. Grishin N.V. Fold change in evolution of protein structures. J. Struct. Biol. 134 (2001) 167-185
19. Gruber M., Söding J., and Lupas A.N. Comparative analysis of coiled-coil prediction methods. J. Struct. Biol. 155 (2006) 140-145
20. Humphrey W., Dalke A., and Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 14 (1996) 33-38
21. Iyer L.M., Leipe D.D., Koonin E.V., and Aravind L. Evolutionary history and higher order classification of AAA+ ATPases. J. Struct. Biol. 146 (2004) 11-31
22. Johnson, G, 1997. Designing Life: Proteins 1, Computers 0. The New York Times. March 25.
23. Jones D.T., Miller R.T., and Thornton J.M. Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Proteins 23 (1995) 387-397
24. Judson H.F. The Eighth Day of Creation (1996), Cold Spring Harbor Laboratory Press
25. Kajava A.V. Proteins with repeated sequence-Structural prediction and modeling. J. Struct. Biol. 134 (2001) 132-144
26. Kajava A.V., Gorbea C., Ortega J., Rechsteiner M., and Steven A.C. New HEAT-like repeat motifs in proteins regulating proteasome structure and function. J. Struct. Biol. 146 (2004) 425-430
27. Kalidas Y., and Chandra N. PocketDepth: a new depth based algorithm for identification of ligand binding sites in proteins. J. Struct. Biol. 161 (2008) 31-42
28. Kryshtafovych A., Venclovas C., Fidelis K., and Moult J. Progress over the first decade of CASP experiments. Proteins 61 Suppl. 7 (2005) 225-236
29. Kryshtafovych A., Fidelis K., and Moult J. Progress from CASP6 to CASP7. Proteins 69 Suppl. 8 (2007) 194-207
30. Lei H., Wu C., Liu H., and Duan Y. Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations. Proc. Natl. Acad. Sci. USA 104 (2007) 4925-4930
31. Lensink M.F., Méndez R., and Wodak S.J. Docking and scoring protein complexes: CAPRI 3rd Edition. Proteins 69 (2007) 704-718
32. Levinthal C. Are there pathways for protein folding?. J. Chim. Phys. 65 (1968) 44-45
33. Lupas A.N., Ponting C.P., and Russell R.B. On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?. J. Struct. Biol. 134 (2001) 191-203
34. Lupas A.N., and Koretke K.K. Bioinformatic analysis of ClpS, a protein module involved in prokaryotic and eukaryotic protein degradation. J. Struct. Biol. 141 (2003) 77-83
35. McLachlan A.D. Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551. J. Mol. Biol. 61 (1971) 409-424
36. McLachlan A.D. Repeating sequences and gene duplication in proteins. J. Mol. Biol. 64 (1972) 417-437
37. McLachlan A.D. Gene duplication and the origin of repetitive protein structures. Cold Spring Harb. Symp. Quant. Biol. 52 (1987) 411-420
38. McRee D.E. XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density. J. Struct. Biol. 125 (1999) 156-165
39. McRee D.E., and Israel M. Xtal View, Protein Structure Solution and Protein Graphics, a Short History. J. Struct. Biol. 163 (2008) 208-213
40. Meier M., Lustig A., Aebi U., and Burkhard P. Removing an interhelical salt bridge abolishes coiled-coil formation in a de novo designed peptide. J. Struct. Biol. 137 (2002) 65-72
41. Moult J. Comparative modeling in structural genomics. Structure 16 (2008) 14-16
42. Moult J., Hubbard T., Bryant S.H., Fidelis K., and Pedersen J.T. Critical assessment of methods of protein structure prediction (CASP): round II. Proteins Suppl. 1 (1997) 2-6
43. Offer G., Hicks M.R., and Woolfson D.N. Generalized Crick equations for modeling noncanonical coiled coils. J. Struct. Biol. 137 (2002) 41-53
44. Parry D.A. Coiled-coils in alpha-helix-containing proteins: analysis of the residue types within the heptad repeat and the use of these data in the prediction of coiled-coils in other proteins. Biosci. Rep. 2 (1982) 1017-1024
45. Pauling L., and Corey R.B. Two hydrogen-bonded spiral configurations of the polypeptide chain. J. Am. Chem. Soc. 72 (1950) 5349
46. Pauling L., and Corey R.B. The pleated sheet, a new layer configuration of polypeptide chains. Proc. Natl. Acad. Sci. USA 37 (1951) 251-256
47. Pauling L., Corey R.B., and Branson H.R. The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain. Proc. Natl. Acad. Sci. USA 37 (1951) 235-240
48. Pauling L., and Corey R.B. Compound helical configurations of polypeptide chains: structure of proteins of the α-keratin type. Nature 171 (1953) 59-61
49. Pokala N., and Handel T.M. Protein design-where we were, where we are, where we're going. J. Struct. Biol. 134 (2001) 269-281
50. Punta M., Forrest L.R., Bigelow H., Kernytsky A., Liu J., and Rost B. Membrane protein prediction methods. Methods 41 (2007) 460-474
51. Ramachandran G.N., and Kartha G. Structure of collagen. Nature 176 (1955) 593-595
52. Ramachandran G.N., Ramakrishnan C., and Sasisekharan V. Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7 (1963) 95-99
53. Ramshaw J.A.M., Shah N.K., and Brodsky B. Gly-X-Y tripeptide frequencies in collagen: a context for host-guest triple-helical peptides. J. Struct. Biol. 122 (1998) 86-91
54. Rost B. Protein secondary structure prediction continues to rise. J. Struct. Biol. 134 (2001) 204-218
55. Rost B., and Sander C. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232 (1993) 584-599
56. Sanbonmatsu K.Y., and Tung C.S. High performance computing in biology: multimillion atom simulations of nanoscale systems. J. Struct. Biol. 157 (2007) 470-480
57. Sanger F., Thompson E.O., and Kitai R. The amide groups of insulin. Biochem. J. 59 (1955) 509-518
58. Schulman E. A Briefer History of Time (1999), W.H. Freeman, New York
59. Shirts M., and Pande V.S. Screen savers of the world unite!. Science 290 (2000) 1903-1904
60. Simons K.T., Bonneau R., Ruczinski I., and Baker D. Ab initio protein structure prediction of CASP III targets using ROSETTA. Proteins Suppl. 3 (1999) 171-176
61. Sippl M.J. Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5 (1995) 229-235
62. Söding J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21 (2005) 951-960
63. Sonnhammer E.L., von Heijne G., and Krogh A. A hidden Markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol. 6 (1998) 175-182
64. Strelkov S.V., and Burkhard P. Analysis of alpha-helical coiled coils with the program TWISTER reveals a structural mechanism for stutter compensation. J. Struct. Biol. 137 (2002) 54-64
65. Wang Y., Rader A.J., Bahar I., and Jernigan R.L. Global ribosome motions revealed with elastic network model. J. Struct. Biol. 147 (2004) 302-314
66. Weiner P.K., and Kollman P.A. AMBER: assisted model building with energy refinement. A general program for modeling molecules and their interactions. J. Comp. Chem. 2 (1981) 287-303
67. Wilbur W.J., and Lipman D.J. Rapid similarity searches of nucleic acid and protein data banks. Proc. Natl. Acad. Sci. USA 80 (1983) 726-730