Molecular conformation search by distance matrix perturbations

Journal of Mathematical Chemistry

Volumn 37, Issue 3, 2005, Pages 233-253

  Emiris, Ioannis Z ^a   Nikitopoulos, Theodoros G ^b  

^a UNIVERSITY OF ATHENS   (Greece)

^b UNIVERSITY OF CRETE   (Greece)

Author keywords

Distance geometry; Local conformation search; Matrix perturbation; Singular value

Indexed keywords

ALGORITHM; CHEMICAL STRUCTURE; COMPUTER AIDED DESIGN; CONFERENCE PAPER; CONFORMATION; CONFORMATIONAL TRANSITION; CRYSTALLIZATION; DRUG DESIGN; GEOMETRY; MOLECULAR MECHANICS; NUCLEAR MAGNETIC RESONANCE; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; TECHNIQUE; THREE DIMENSIONAL IMAGING; VALIDATION PROCESS; X RAY CRYSTALLOGRAPHY;

EID: 17744384497     PISSN: 02599791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10910-004-1466-4     Document Type: Article

References (37)

1. N. Gō H.A. Scheraga 1979 Macromolecules 3 178
2. Q. Dong Z. Wu 2003 J. Global Optimization 26 321
3. P. Guntert C. Mumenthaler K. Wuthrich 1997 J. Mol. Biol. 273 283
4. S. LeGrand A. Elofsson D. Eisenberg 1996 H. Bohr S. Brunak Protein Folds: A Distance Based Approach CRC Press Boca Raton, FL
5. National Research Council 1995 Mathematical Challenges from Theoretical/Computational Chemistry National Academy Press Washington, DC
6. C. Bailey-Kellogg A. Widge J.J. Kelley III M.J. Berardi J.H. Bushweller B.R. Donald 2000 J. Comp. Biol. 7 537
7. T.E. Malliavin P. Barthe M.A. Delsuc 2001 Theor. Chem. Acc. 106 91
8. L.M. Blumenthal 1970 Theory and Applications of Distance Geometry 2nd ed. Chelsea Publishing Company Bronx, NY Vol. 15
9. T.F. Havel 1998 P. von Ragué P.R. Schreiner N.L. Allinger T. Clark J. Gasteiger P.A. Kollman H.F. Schaefer III Encyclopedia of Computational Chemistry Wiley New York 723 742
10. J.M. Blaney, G.M. Crippen, A. Dearing and J.S. Dixon, DGEOM: program #590, Quantum Chemistry Program Exchange, 1990. http://qcpe.chem.indiana.edu.
11. I.D. Kuntz J.F. Thomason C.M. Oshiro 1993 N.J. Oppenheimer T.L. James Methods in Enzymology Academic Press Boston 159 204 Vol. 177
12. A.W.M. Dress T.F. Havel 1988 Discr. Appl. Math. 19 129
13. T. Malliavin and F. Dardel, in: Sciences Fondamentales, Vol. AF (Techniques de l'Ingénieur, Paris, 2002) pp. 6608 (1-18).
14. P.M. Pardalos X. Lin 1997 F. Giannessi S. Komlósi T. Rapcsák New Trends in Mathematical Programming Kluwer Boston
15. J. Moré Z. Wu 1999 J. Global Optimization 15 219
16. G.M. Crippen 1992 J. Comp. Chem. 13 351
17. Quantum Chemistry Program Exchange, http://qcpe.chem.indiana.edu.
18. Conformational Searching and Analysis Software, http://www.netsci.org/ resources/software/modeling/conf.
19. I.Z. Emiris B. Mourrain 1999 Algorithmica, special issue on algorithms for computational biology 25 372
20. T.F. Havel I. Najfeld 1995 J. Fleischer J. Grabmeier W. Hehl W. Küchlin Computer Algebra in Science and Engineering World Scientific Publishing Singapore 243 259
21. D. Manocha Y. Zhu W. Wright 1995 Comp. Appl. Biol. Sci. 11 71
22. W.J. Wedemeyer H.A. Scheraga 1999 J. Comput. Chem. 20 819
23. J.B. Saxe, in: Proceedings of the 17th Allerton Conference on Communications, Control and Computing (1979) pp. 480-489.
24. R. Mathar 1985 Linear Algebra Appl. 67 1
25. M. Bakonyi C.R. Johnson 1995 SIAM J. Matrix Anal. Appl. 16 646
26. J.W. Demmel 1992 SIAM J. Matrix Anal. Appl. 13 10
27. M.A. Wicks R.A. Decarlo 1995 SIAM J. Matrix Anal. Appl. 16 123
28. D. Bini V.Y. Pan 1994 Polynomial Matrix Computations, Vol. 1, Fundamental Algorithms Birkhäuser Boston
29. G.H. Golub C.F. Van Loan 1996 Matrix Computations 3rd ed. The Johns Hopkins University Press Baltimore, Maryland
30. G.W. Stewart J. Sun 1990 Matrix Perturbation Theory Academic Press Boston
31. A.I. Barvinok 1995 Discr. Comput. Geom. 13 189
32. Y.Z. Xu Q. Ouyang J.G. Wu J.A. Yorke G.X. Xu D.F. Xu R.D. Soloway J.Q. Ren 2000 J. Comput. Chem. 21 1101
33. J. Kuszewski M. Nilges A.T. Brünger 1992 J. Biomolecular NMR 2 33
34. E. Anderson Z. Bai C. Bischof J. Demmel J. Dongarra J. Du Croz A. Greenbaum S. Hammarling A. McKenney S. Ostrouchov D. Sorensen 1995 LAPACK Users' Guide 2nd ed. SIAM Philadelphia
35. J-P. Merlet, in: Proc. Conf. Systèmes d'Equations Algébriques (Toulouse, 2000).
36. P.L. Easthope T.F. Havel 1989 Bull. Math. Biol 51 173
37. I. Dhillon, G. Fann and B. Parlett, in: Proc. 8th SIAM Conf. Parallel Proces. Scient. Comp., eds. M. Heath, V. Torczon, G. Astfalk, P.E. Bjørstad, A.H. Karp, C.H. Koebel, V. Kumar, R.F. Lucas, L.T. Watson and D.E. Womble (SIAM, Philadelphia, 1997) pp. 383-389.