The increasing availability of high-performance com puters makes it possible to treat larger systems in shorter computing times. However, a more challeng ing aspect of the availability of larger and faster com puters is the exploration of alternative algorithms. This is especially important in view of new computer archi tectures. In this work we describe a novel technique for feedback-scaling individual NOE distance restraints during molecular-dynamics-simulated annealing ex periments.
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References
1.
Baker, J.K.1992. Nuclear overhauser effect spectroscopy (NOESY) and dihedral angle measurements in the determination of the conformation of taxol in solutionSpectroscopy Lett.25(1):31-48.
2.
Brünger, A.T.1990. Refinement of three-dimensional structures of proteins and nucleic acids In Molecular Dynamics. Applications in Molecular Biology, edited by J. M. Goodfellow. Boca Raton: ECRC Press, pp. 137-178.
3.
Cachau, R.E., Serpersu, E.H., Mildvan, A.S., August, J.T., and Amzel, L.M.1989. Recognition in cell adhesion. A comparative study of the conformations of RGD-containing peptides by Monte Carlo and NMR methodsJ. Mol. Recog.2:179-186.
4.
Castellano, E.E., and Hodder, O.J.R.1973. The crystal and molecular structure of the diterpenoid baccatin V, a naturally occurring oxetan with taxane skeleton.Acta Cryst. B29:2566-2570.
5.
Chmurny, G.N., Hilton, B.D., Brobst, S., Look, S.A., Whiterup, K.M., and Beutler, J.A.1992. 1H- and 13C-NMR assignments for taxol, 7-epitaxol, and cephalomannineJ. Nat. Prod.55(8): 1157-1161.
6.
Falzone, J., Benesik, A.J., and Lecomte, J.T.J.1992. Characterization of taxol in methylene chloride by NMR spectroscopyTetrahed. Lett . 33(9): 1169-1172.
7.
Fesik, S.W., Gampe Jr., R.T., Holzman, T.F., Egan, D.A., Edalji, R., Luly, J.R., Simmer, R., Helfrich, R., Kishore, V., and Rich, D.H.1990. Isotope-edited NMR of Cyclosporin A bound to Cyclophilin: Evidence for a trans 9,10 amide bondScience250:1406-1410.
8.
Gueritte-Voegelein, F., Guenard, D., Mangatal, L., Potier, P., Guilhem, J., and Cesario, M.1990. Structure of a synthetic taxol precursor: N-tert-Butoxycarbonyl-10-deacetyl-N-debenzoyltaxolActa Cryst.C46:781-784.
9.
Gueritte-Voegelein, F., Guenard, D., Lavelle, F., Le Goff, M-.T., Mangatal, L., and Potier, P. 1991.
10.
Relationships between the structure of taxol analogues and their antimitotic activityJ. Med. Chem.34:992-998.
11.
Hagler, A.T., Lifson, S., and Dauber, P.1979. Consistent force field studies of intermolecular forces in hydrogen-bonded crystals. 2. A benchmark for the objective comparison of alternative force fieldsJ. Am. Chem. Soc.101:5122-5130;
12.
DISCOVER version 2.7.0 (March 1991), BIOSYM Technologies, 10065 Barnes Canyon Road, San Diego, CA 92121, USA.
13.
Hilton, B. D., Chmurny, G. N., and Muschik,
14.
G.M.1992. Taxol: quantitative internuclear proton-proton distances in CDCl3 solution from nOe data: 2D NMR ROESY buildup rates at 500MHzJ. Nat. Prod.55(8):1157-1161.
15.
Holmes, F.A., Walters, R.S., Theriault, R.L., Forman, A.D., Newton, L.K., Raber, M.N., Buzdar, A.U., Frye, D.K., and Hortobagyi, G.N.1991. Phase II trial of taxol, an active drug in the treatment of metastatic breast cancerJ. Natl. Cancer Inst.83(24): 1797-1802.
16.
Horwitz, S.B.1992. Mechanism of action of taxolTrends Pharm. Sci.13:134-137.
17.
Kingston, D.G.I., Samaranayake, G.C., and Ivey, A.1990. The chemistry of taxol, a clinically useful anticancer agentJ. Nat. Prod.53(1):1-12.
18.
Kingston, D.G.I.1991. The chemistry of taxolPharmac. Ther.52:1-34.
19.
McGuire, W.P., Rowinsky, E.K., Rosenshein, N.B., Grumbine, F.C., Ettinger, D.S., Armstrong, D.K., and Donehower, R.C.1989. Taxol: A unique antineoplasic agent with significant activity in advanced ovarian epithelial neoplasmsAnn. Intern. Med.111:273-279.
20.
Samaranayake, G., Magri, N.F., Jitrangsri, C., and Kingston, D.G.I.1991. Modified taxols. 5. Reaction of taxol with electrophilic reagents and preparation of a rearranged taxol derivative with tubulin assembly activityJ. Org. Chem.56:5114-5119.
21.
Scheek, R.M., van Gunsteren, W.F., and Kaptein, R.1989. Molecular dynamics simulation techniques for determination of molecular structures from nuclear magnetic resonance data In Methods in Enzyrnology. Vol. 177 Part B, Nuclear Magnetic Resonance, edited by J. N. Abelson and M. I. Simon. San Diego: Academic Press Inc., pp. 204-282.
22.
Schiff, P.B., Fant, J., and Horwitz, S.B.1979. Promotion of microtubule assembly in vitro by taxolNature277:665-667.
23.
Schiff, P.B., and Horwitz, S.B.1980. Taxol stabilizes microtubules in mouse fibroblast cellsProc. Natl. Acad. Sci. USA77:1561-1565.
24.
Stewart, J.J.P.1990. MNDO A semiempirical molecular orbital programJ. Comp.-Aid. Mol. Des. 4(1):1-101.
25.
Swindell, C.S., Krauss, N.E., Horwitz, S.B., and Ringel, I.1991. Biologically active taxol analogues with deleted A-ring side chain substituents and variable C-2' configurationsJ. Med. Chem.34:1176-1184.
26.
Van Duyne, G.D., Standaert, R.F., Karplus, P.A., Schreiber, S.L., and Clardy, J.1991. Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complexScience252: 839-843.
27.
Wani, M.C., Taylor, H.L., Wall, M.E., Coggon, P., and McPhail, A.T.1971. Plant antitumor agents. VI. The isolation and structure of taxol, a novel antileukemic and antitumor agent from Taxus BrevifoliaJ. Am. Chem. Soc.93:2325-2327.
28.
Withka, J.M., Swaminathan, S., Srinivasan, J., Beveridge, D.L., and Bolton, P.H.1992. Toward a dynamical structure of DNA: Comparison of theoretical and experimental NOE intensitiesScience255: 597-601.