Protein folding by motion planning

Physical Biology

Volumn 2, Issue 4, 2005, Pages

  Thomas, Shawna ^a   Song, Guang ^b   Amato, Nancy M ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

^b IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

CONFERENCE PAPER; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MONTE CARLO METHOD; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; ROBOTICS; STRUCTURE ANALYSIS;

EID: 27744446287     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/2/4/S09     Document Type: Conference Paper

References (25)

1. Levitt M, Gerstein M, Huang E, Subbiah S and Tsai J 1997 Protein folding: the endgame Annu. Rev. Biochem. 66 549-79
2. Reeke G N Jr 1988 Protein folding: computational approaches to an exponential-time problem Annu. Rev. Comput. Sci. 3 59-84
3. Lansbury P T 1999 Evolution of amyloid: what normal protein folding may tell us about fibrillogenesis and disease Proc. Natl Acad. Sci. USA 96 3342-4
4. Amato N M and Song G 2002 Using motion planning to study protein folding pathways J. Comput. Biol. 9 149-68 (Special issue of Int. Conf. Comput. Mol. Biol. (RECOMB) 2001)
5. Kavraki L E, Svestka P, Latombe J C and Overmars M H 1996 Probabilistic roadmaps for path planning in high-dimensional configuration spaces IEEE Trans. Robot. Autom. 12 566-80
6. Song G and Amato N M 2001 A motion planning approach to folding: from paper craft to protein folding Proc. IEEE Int. Conf. Robot. Autom. (ICRA) pp 948-53
7. Li R and Woodward C 1999 The hydrogen exchange core and protein folding Protein Sci. 8 1571-91
8. Dobson C M, Sali A and Karplus M 1998 Protein folding: a perspective from theory and experiment Angew. Chem. Int. Ed. 37 868-93
9. Radford S E and Dobson C M 1995 Insights into protein folding using physical techniques: studies of lysozyme and α-lactalbumin Phil. Trans. R. Soc. Lond. B 348 17
10. Bryngelson J D, Onuchic J N, Socci N D and Wolynes P G 1995 Funnels, pathways, and the energy landscape of protein folding: A synthesis Protein Struct. Funct. Genet. 21 167-95
11. Song G, Thomas S L, Dill K A, Scholtz J M and Amato N M 2003 A path planning-based study of protein folding with a case study of hairpin formation in proteins G and L Proc. Pacific Symposium of Biocomputing (PSB) pp 240-51
12. Sternberg M J 1996 Protein Structure Prediction (Oxford: OIRL Press at Oxford University Press)
13. The IMB Jena Image Library of Biological Macromolecules http://www.imb-jena.de - ref-separator -
14. Bayazit O B, Song G and Amato N M 2001 Ligand binding with OBPRM and haptic user input: enhancing automatic motion planning with virtual touch Proc. IEEE Int. Conf. Robot. Autom. (ICRA) pp 954-9 (This work was also presented as a poster at RECOMB 2001)
15. Singh A P, Latombe J C and Brutlag D L 1999 A motion planning approach to flexible ligand binding 7th Int. Conf. on Intelligent Systems for Molecular Biology (ISMB) pp 252-61
16. Song G and Amato N M 2001 Using motion planning to study protein folding pathways Proc. Int. Conf. Comput. Mol. Biol. (RECOMB) pp 287-96
17. Fiebig K M and Dill K A 1993 Protein core assembly processes J. Chem. Phys. 98 3475-87
18. Levitt M 1983 Protein folding by restrained energy minimization and molecular dynamics J. Mol. Biol. 170 723-64
19. Lazaridis T and Karplus M 1999 Effective energy function for proteins in solution Proteins 35 133-52 (http://mingus.sci.ccny.cuny.edu/server/)
20. The Protein Data Bank http://www.rcsb.org/pdb/ - ref-separator -
21. Munoz V and Eaton W A 1999 A simple model for calculating the kinetics of protein folding from three dimensional structures Proc. Natl Acad. Sci. USA 96 11311-6
22. Alm E and Baker D 1999 Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures Proc. Natl Acad. Sci. USA 96 11305-10
23. Dill K A, Fiebig K M and Chan H S 1993 Cooperativity in protein-folding kinetics Proc. Natl Acad. Sci. USA 90 1942-6
24. McCallister E L, Alm E and Baker D 2000 Critical role of β-hairpin formation in protein G folding Nat. Struct. Biol. 7 669-73
25. Kim D E, Fisher C and Baker D 2000 A breakdown of symmetry in the folding transition state of protein l J. Mol. Biol. 298 971-84