Computational analysis of sequence selection mechanisms

Structure

Volumn 12, Issue 4, 2004, Pages 547-557

  Meyerguz, Leonid ^a   Grasso, Catherine ^b   Kleinberg, Jon ^a   Elber, Ron ^a  

^a Department of Computer Science and School of Operations Research and Information Engineering   (United States)

^b Department of Obstetrics Gynecology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BULK DENSITY; ENERGY TRANSFER; ENTROPY; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SURVIVAL RATE; TEMPERATURE;

COMPUTER SIMULATION; DATABASES, PROTEIN; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; PROTEIN FOLDING; SELECTION (GENETICS); TEMPERATURE; THERMODYNAMICS;

EID: 1842450481     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.str.2004.02.018     Document Type: Article

References (25)

1. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Rapp B.A., Wheeler D.L. GeneBank. Nucleic Acids Res. 28:2000;15-18.
2. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein data bank. Nucleic Acids Res. 28:2000;235-242.
3. Betancourt M.R., Thirumalai D. Pair potentials for protein folding. choice of reference states and sensitivity of predicted states to variations in the interaction schemes Protein Sci. 2:1999;361-369.
4. Betancourt M.R., Thirumalai D. Protein sequence design by energy landscaping. J. Phys. Chem. 106:2002;599-609.
5. Feynmann R.P. Statistical Mechanics. a Set of Lectures:1982;Benjamin, Reading, Massachusetts.
6. Huynen M.A., Stadler P.F., Fontana W. Smoothness within ruggedness. the role of neutrality in adaptation Proc.Natl. Acad. Sci. USA. 93:1996;397-401.
7. Jerrum M., Sinclair A. The Markov chain Monte Carlo method. an approach to approximate counting and integration Hochbaum D.S. Approximation Algorithms for NP-Hard Problems. 1996;482-520 PWS, Boston.
8. Kabsch W. Discussion of solution for the best rotation to relate 2 sets of vectors. Acta Crytsllogr. A. 34:1978;827-828.
9. Karchin R., Cline M., Mandel-Gutfreund Y., Karplus K. Hidden Markov models that use predicted local structure for fold recognition. alphabets of backbone geometry Proteins. 51:2003;504-514.
10. Kleinberg J. Efficient algorithms for protein sequence design and the analysis of certain evolutionary fitness landscapes. J. Comput. Biol. 6:1999;387-404.
11. Koehl P., Levitt M. Protein topology and stability define the space of allowed sequences. Proc. Natl. Acad. Sci. USA. 99:2002;1280-1285.
12. Kumar S., Tsai C.J., Nussinov R. Temperature range of thermodynamic stability for the native state of reversible two-state proteins. Biochemistry. 42:2003;4864-4873.
13. Larson S.M., England J.L., Desjarlais J.R., Pande V.S. Thoroughly sampling sequence space. large-scale protein design of structural ensembles Protein Sci. 11:2002;2804-2813.
14. Lau K.F., Dill K. Theory for protein mutability and biogenesis. Proc. Natl. Acad. Sci. USA. 87:1990;638-642.
15. Lipman D., Wilbur W. Modelling the neutral and selective evolution of protein folding. Proc. R Soc. Lond. B Biol. Sci. 245:1991;7-11.
16. Maynard S.J. Natural selection and the concept of protein space. Nature. 225:1970;563-564.
17. Meller J., Elber R. Linear optimization and a double statistical filter for protein threading protocols. Proteins. 45:2001;241-261.
18. Meller J., Elber R. Protein recognition by sequence-to-structure fitness. bridging efficiency and capacity of threading models Advances in Chemical Physics. F. Richard. 2002;77-130 John Wiley & Sons, New York.
19. Saven J.G. Combinatorial protein design. Curr. Opin. Struct. Biol. 12:2002;453-458.
20. Saven J.G., Wolynes P.G. Statistical mechanics of the combinatorial synthesis and analysis of folding macromolecules. J. Phys. Chem. B. 101:1997;8375-8389.
21. Shakhnovich E.I. Proteins with selected sequences fold into a unique native conformations. Phys. Rev. Lett. 72:1994;3907-3911.
22. Shakhnovich E.I., Gutin A.M. A new approach to the design of stable proteins. Protein Eng. 6:1993;793-800.
23. Shindyalov I.N., Bourne P.E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11:1998;739-747.
24. Tobi D., Elber R. Distance dependent, pair potential for protein folding. results from linear optimization Proteins. 41:2000;40-46.
25. Torrie G.M., Valleau J.P. Nonphysical sampling distributions in Monte-Carlo free energy estimation. umbrella sampling J. Comp. Phys. 23:1977;187-199.