Complete maps of molecular-loop conformational spaces

Journal of Computational Chemistry

Volumn 28, Issue 13, 2007, Pages 2170-2189

  Porta, Josep M ^a   Ros, Lluís ^a   Thomas, Federico ^a   Corcho, Francesc ^b   Cantó, Josep ^b   Pérez, Juan Jesús ^b  

^a INSTITUT DE ROBÒTICA I INFORMÀTICA INDUSTRIAL CSIC UPC   (Spain)

^b UNIVERSITAT POLITÈCNICA DE CATALUNYA   (Spain)

Author keywords

Adamantane; B zier clipping; Bicyclohexane; Bound smoothing; Cayley Menger determinant; Complete method; Conformational space; Cycloheptane; Cyclooctane; Disulfide bond; Loop closure; Ring; Seven atom loop; Tripeptide loop

Indexed keywords

ATOMIC PHYSICS; CONFORMATIONS; MOLECULAR INTERACTIONS; NUMERICAL METHODS; SET THEORY;

BICYCLOHEXANE; CAYLEY-MENGER DETERMINANTS; COMPLETE METHODS; CONFORMATIONAL SPACES; CYCLOHEPTANE; CYCLOOCTANE; DISULFIDE BONDS; SEVEN-ATOM LOOPS; TRIPEPTIDE LOOP;

MOLECULAR STRUCTURE;

EID: 34547930859     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20733     Document Type: Article

References (54)

1. Gō, N.; Scheraga, H. A. Macromolecules 1970, 3(2), 178.
2. Wedemeyer, W. J.; Scheraga, H. J Comput Chem 1999, 20(8), 819.
3. Gibson, K. D.; Scheraga, H. A. J Comput Chem 1997, 18(3), 403.
4. Coutsias, E. A.; Seok, C.; Jacobson, M. P.; Dill, K. A. J Comput Chem 2004, 25(4), 510.
5. Coutsias, E. A.; Seok, C.; Jacobson, M. P.; Dill, K. A. Int J Quant Chem 2006, 106(1), 176.
6. Crippen, G. M.; Havel, T. F. Distance Geometry and Molecular Conformation; Research Studies Press: Taunton, England, 1988.
7. Havel, T. F. In Encyclopedia of Computational Chemistry, von Ragué, P.; Schreiner, P. R.; Allinger, N. L.; Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer, H. F., III. Eds.; Wiley, 1998; pp. 723-742.
8. Porta, J. M.; Ros, L.; Thomas, F. In Proceedings of the IEEE International Conference on Robotics and Automation; 2005; pp. 960-967.
9. Saxe, J. B. In Proceedings of the 17th Allerton Conference in Communications, Control and Computing, 1979; pp. 480-489.
10. Blumenthal, L. M. Theory and Applications of Distance Geometry; Oxford University Press, 1953.
11. Sippl, M. J.; Scheraga, H. Proc Nat Acad Sci 1986, 83, 2283.
12. Whiteley, W. Phys Biol 2005, 2, 116.
13. Flexweb server, http://flexweb.asu.edu.
14. Jacobs, D.; Rader, A. J.; Kuhn, L.; Thorpe, M. Proteins 2001, 44, 150.
15. Thorpe, M.; Lei, M.; Rader, A. J.; Jacobs, D. J.; Kuhn, L. J Mol Graph Model 2001, 19, 60.
16. ProFlex web page, http://www.bch.msu.edu/labs/kuhn/web/software.html.
17. Go, N.; Scheraga, H. A. J Chem Phys 1969, 51, 4751.
18. Pieper, D. The Kinematics of Manipulators under Computer Control; Ph.D. Thesis; Stanford University, 1968.
19. Roth, B.; Rastegar, J.; Scheinman, V. In On the Theory and Practice of Robot Manipulators; First CISM IFTOMM Symposium; 1973; pp. 93-113.
20. Shenkin, P. S.; Yarmush, D. L.; Fine, R. M.; Wang, H. J.; Levinthal, C. Biopolymers 1987, 26, 2053.
21. Hong, M.; Scheraga, H. A. Encyclopedia of Computational Chemistry, Vol. 5; Wiley, 1998; pp. 552-556.
22. Canutescu, A. A.; Dunbrack, R. L. Prot Sci 2003, 12, 963.
23. Lee, H.-Y.; Liang, C.-G. Mech Mach Theor 1988, 23(3), 209.
24. Raghavan, M.; Roth, B. Trans ASME J Mech Des 1993, 115, 502.
25. Lin, W.; Duffy, J.; Griffis, M. ASME J Mech Des 1994, 114, 444.
26. Griffis, M.; Duffy, J. J Robotic Syst 1989, 6, 703.
27. Porta, J. M.; Ros, L.; Thomas, F.; Torras, C. IEEE Trans Robot 2005, 21(2), 176.
28. Tsai, L.-W.; Morgan, A. ASME J Mech Transm Autom Des 1985, 107, 189.
29. Primrose, E. J. F. Mech Mach Theor 1986, 21(6), 509.
30. Manocha, D.; Canny, J. IEEE Trans Robot Autom 1994, 10(5), 648.
31. Dixon, A. L. Proc Lond Math Soc 1908, 6(2), 468.
32. Emiris, I. Z.; Canny, J. J Symbolic Comput 1995, 20(2), 117.
33. Sommese, A. J.; Wampler, C. W. The Numerical Solution of Systems of Polynomials Arising in Engineering and Science; World Scientific, 2005.
34. Bombín, C.; Ros, L.; Thomas, F. In Advances in Robot Kinematics; Lenarci, J.; Stanisic, M. M.; Eds; Kluwer, 2000; pp. 53-60.
35. Bombín, C.; Ros, L.; Thomas, F. In Proceedings of the IEEE International Conference on Robotics and Automation, 2001; Vol. 3; pp. 3332-3337.
36. Zhang, M.; White, R. A.; Wang, L.; Goldman, R.; Kavraki, L.; Hassen, B. Bioinformatics 2005, 21(5), 624.
37. Cayley, A. Camb Math J 1841, II, 267.
38. Menger, K. Am J Math 1931, 53, 721.
39. Sippl, M. J.; Scheraga, H. Proc Nat Acad Sci 1985, 82, 2197.
40. Sherbrooke, E. C.; Patrikalakis, N. M. Comput Aided Geomet Des 1993, 10, 379.
41. Dress, A. W. M.; Havel, T. Discrete Appl Math 1988, 19, 129.
42. Rajan K.; Deo N. Bull Math Biol 1999, 61(5), 987.
43. Farm, G. Curves and Surfaces for Computer Aided Geometric Design - A Practical Guide; Academic Press, 1990.
44. Morgan, A.; Shapiro, V. ACM Trans Math Software 1987, 13(2), 152.
45. Farouki, R. T.; Rajan, V. T. Comput Aided Geomet Des 1987, 10, 379.
46. Karmarkar, N. K. Combinatorica 1984, 4, 373.
47. Borcea, C.; Streinu, I. Discrete Comput Geometry 2004, 31(2), 287.
48. Message Passing Interface web page, http://www-unix.mcs.anl.gov/mpi/ index.htm.
49. Makhorin, A.; GLPK-the GNU linear programming toolkit, http://www.gnu.org/software/glpk.
50. Crippen, G. J Comput Chem 1992, 13(3), 351.
51. Kolossváry, I.; Guida, W. J Am Chem Soc 1993, 115, 2107.
52. Rocha, W. R.; Pliego, J. R.; Resende, S. M.; Dos Santos, H. F.; De Oliveira, M. A.; De Almeida, W. B. J Comput Chem 1998, 19(5), 524.
53. Barcelona Supercomputing Center web page, http://www.bsc.es.
54. Emiris, I. Z.; Mourrain, B. Algorithmica 1999, 25(2-3), 372.