|
 REFERENCES
Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.
| |
1
|
V. Abkeviech, A. Gutin, and E. Shakhnovich. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemestry, 33:10026 - 10036, 1994.
|
| |
2
|
N. Alexandrov. Structural argument for N-terminal initiation of protein folding. Protein Sci., 2:1989 - 1991, 1993.
|
| |
3
|
|
| |
4
|
E. Bornberg-Bauer. Random Structures and the Evolution of Biopolymers. PhD thesis, University of Vienna, 1995.
|
| |
5
|
E. Bornberg-Bauer. Random structures and evolution of biopolymers: A computational case study on RNA secondary structures. Pharm. Acta Helv., 71:79-85, 1996.
|
| |
6
|
E. Bornberg-Bauer. Structure formation of biopolymers is complex, their evolution may be simple. In L. Hunter and T. Klein, editors, Proceedings of the Pacific Symposium on Biocomputing, pages 97 - 108. World Scientific, London, 1996.
|
| |
7
|
E. Bornberg-Bauer and A. Renner. tofolapo-0.07, available upon request from bornberg@dkfz-heidelberg.de.
|
| |
8
|
H. S. Chan and K. A. Dill. The protein folding problem. Physics today, 2:24 - 32, 1993.
|
| |
9
|
H. S. Chan and K. A. Dill. Comparing folding codes for proteins and polymers. Proteins Struct. Funct. Gen., 24:335 - 344, 1996.
|
| |
10
|
C. Chothia. One thousand families for the molecular biologist. Nature, 357:543 - 544, 1992.
|
| |
11
|
M. H. Cordes, A. R. Davidson, and R. T. Sauer. Sequence space, folding and protein design. Curr. Opn. Struct. Biol., 6:3- 10, 1996.
|
| |
12
|
G. M. Crippen. Prediction of protein folding from amino acid sequence over discrete conformation spaces. Biochemistry, 30:4232 - 4237, 1991.
|
| |
13
|
K. A. Dill. Dominant forces in protein folding. Biochemistry, 29:7133 - 7155, 1990.
|
| |
14
|
K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan. Principles of protein folding - a perspective from simple exact models. Protein Sci., 4:561 -602, 1995.
|
| |
15
|
K. M. Fiebig and K. A. Dill. Protein core assembly process. J. Chem. Phys., 98:3475 - 3487, 1993.
|
| |
16
|
W. Fontana, P. F. Stadler, E. G. Bornberg-Bauer, T. Griesmacher, I. L. Hofacker, M. Tacker, P. Tarazona, E. D. Weinberger, and P. Schuster. RNA folding and combinatory landscapes. Phys. Rev. E, 47:2083- 2099, 1993.
|
| |
17
|
A. Fraenkel. Complexity of protein folding. Bull. Math. Biol., 55:1199- 1210, 1993.
|
| |
18
|
H. Frauenfelder, S. G. Sligar, and P. G. Wolynes. The energy landscape and motions of proteins. Science, 254:1598- 1603, 1991.
|
| |
19
|
W. E. Hart and S. C. Istrail. Fast protein folding in the hydrophobic-hydrophilic model within three-eighths of optimal. J. Comp. Biol., 3:53- 96, 1996.
|
| |
20
|
D. A. Hinds and M. Levitt. Exploring conformation space with a simple lattice model for protein structure. J. Mol. Biol., 243:668- 682, 1994.
|
| |
21
|
E. S. Huang, S. Subbiah, and M. Levitt. Recognizing native folds by the arrangement of hydrophobic and polar residues. J. Mol. Biol., 252:709- 720, 1995.
|
| |
22
|
|
| |
23
|
K. F. Lau and K. A. Dill. A lattice statistical mechanics model of the conformational and sequence spaces of proteins. Macromolecules, 22:3986 - 3997, 1989.
|
| |
24
|
C. Levinthal. Are there pathways fox' protein folding'.? J. Chim. Phys., 65:44 .... 15, 1968.
|
| |
25
|
N. Madras and A. D. Sokal. The pivot algorithm: A highly efficient monte carlo method for the self avoiding-walk. J. ,S'tat. Phys., 50:t09-186, 1987.
|
| |
26
|
E. V. Makeyev, V. A. Kolb, and A. S. Spirin. Enzymatic activity of tl~e ril)osome-bound nascent polypeptide. FEBS Letters, 378:166 .... 170, 1996.
|
| |
27
|
J. Moult and R. Unger. An analysis of protein folding pat.hways. Biochemistry, 30:38/6 - 3824, 1991.
|
| |
28
|
J. T. Ngo and J. Marks. Computational complexity of a t)roblem in molecular structure prediction. Protein Eng., 5:3t3- 321, 1992.
|
| |
29
|
E. M. O'Toole and A. Z. Panagiotopoulos. Monte carlo sinlulation of folding transitions of simple model proteins using a chain growth algorithm. J. Chem. Phys., 97:8644 - 8652, 1992.
|
| |
30
|
A. Renner and E. Bornberg-Bauer. Exploring the fitness landscapes of lattice proteins. In L. Hunter and T. Klein, editors, Proceedings of the Pacific Symposium on Biocornputing. World Scientific, London, in press.
|
| |
31
|
A. Renner, E. Bornberg-Bauer, {. L. H ofacker, and P. F. Stadler. Self-avoiding walk models for non-random heteropolymers, preprint.
|
| |
32
|
M. N. Rosenbluth and A. W. Rosenbluth. Monte carlo calculation of the average extension of molecular chains. J. Chem. Phys., 23:356 - 359, 1954.
|
| |
33
|
A. Salt, E. Shakhnovich, and M. Karplus. Kinetics of protein folding: A lattice model study of the requirements for folding to the native state. J. Mol. Biol., 235' 1614 -- 1636, 1994.
|
| |
34
|
P. Schuster, W. Fontana, P. F. Stadler, and I. L. Hofacker. From sequences to shapes and back: A case study in RNA secondary structures. Proc. Roy.$oc.(London)B, 255:279-284, 1994.
|
| |
35
|
D. Shortle. Protein folding for realists. Protein Sci., 7:991- 1000, 1996.
|
| |
36
|
J. Skolnik and A. Kolinski. Dynamic monte carlo simulations of a new lattice model of globular protein folding, structure and dynamics. J. Mol. Biol., 221:499- 531, 1991.
|
| |
37
|
J. E. Solomon and D. Liney. Exploration of compact protein conformations using the guided replication monte carlo method. Biopolymers, 36:579 - 597, 1995.
|
| |
38
|
P. Stolorz. Recursive approaches to the statistical physiscs of lattice proteins. Proc. ~7th Hawaii International Conference on System Sciences, 1994.
|
| |
39
|
M. Tacker, P. F. Stadler, E. G. Bornberg-Bauer, I. L. Hofacker, and P. Schuster. Algorithm independent properties of RNA secondary structure predictions. Eur. Biophys. J., in press.
|
| |
40
|
T. Thanaraj and P. Argos. Ribosome-mediated translation pause and protein domain organization. Protein Scl., 5:159,t- 1612, 1996.
|
| |
41
|
R. Unger and J. Moult. Finding lowest free energy conformation of a protein is an NP-hard problem: Proof and implications. Bull. Math. Biol., 55:1183- 1198, 1993.
|
| |
42
|
R. Unger and J. Moult. Genetic algorithms for protein folding sinmlations. J. Mol. Biol., 231:75 -81, 1993.
|
| |
43
|
R. Unger and .l. Moult. Local interactions dominate folding in a simple protein model. J. Mol. Biol., 259:988 - 994, t996.
|
| |
44
|
D. B. Wettaufer. Nucleation, rapid folding and globular intrachain regions in proteins. Proc. Natl. Acacl. Sci., USA, 70:697- 701, 1973.
|
| |
45
|
K. Yue, M. Fiebig, P. D. Thomas, H. S. Chan, E. I. Shakhnovich, and K. A. Dill. A test of lattice protein folding algorithms. Proc. Natl. Acad. Sci., USA, 92:325 - 329, 1995.
|
CITED BY 3
|
|
Oswin Aichholzer , David Bremner , Erik D. Demaine , Henk Meijer , Vera Sacristán , Michael Soss, Long proteins with unique optimal foldings in the H-P model, Computational Geometry: Theory and Applications, v.25 n.1-2, p.139-159, May 2003
|
|
|
|
|
|
|
|
Adobe Acrobat
QuickTime
Windows Media Player
Real Player
Pdf
G.2