-
1
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atimic charges: The RESP model
-
Bay, C. I., Cieplak, P., Cornell, W. D., and Kollman, P. A. (1993) A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atimic Charges: The RESP Model. J. Phys. Chem. 97, 10269-10280.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 10269-10280
-
-
Bay, C.I.1
Cieplak, P.2
Cornell, W.D.3
Kollman, P.A.4
-
2
-
-
0027751580
-
Heterodimeric DNA-binding dyes designed for energy transfer: Synthesis and Spectroscopic properties
-
Benson, S. C., Singh, P., and Glazer, A. N. (1993a) Heterodimeric DNA-Binding Dyes Designed for Energy Transfer: Synthesis and Spectroscopic Properties. Nucleic Acids Res. 21, 5727-5735.
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 5727-5735
-
-
Benson, S.C.1
Singh, P.2
Glazer, A.N.3
-
3
-
-
0027756209
-
Heterodimeric DNA-binding dyes designed for energy transfer: Stability and applications of DNA complexes
-
Benson, S. C., Mathies, R. A., and Glazer, A. N. (1993b) Heterodimeric DNA-binding Dyes Designed for Energy Transfer: Stability and Applications of DNA Complexes. Nucleic Acids Res. 21, 5720-5726.
-
(1993)
Nucleic Acids Res.
, vol.21
, pp. 5720-5726
-
-
Benson, S.C.1
Mathies, R.A.2
Glazer, A.N.3
-
4
-
-
0000425457
-
MARDIGRAS-A procedure for matrix analysis of relaxation for discerning geometry of an aqueous structure
-
Borgias, B. A., and James, T. L. (1990) MARDIGRAS-A Procedure for Matrix Analysis of Relaxation for Discerning Geometry of an Aqueous Structure. J. Magn. Reson. 87, 475-487.
-
(1990)
J. Magn. Reson.
, vol.87
, pp. 475-487
-
-
Borgias, B.A.1
James, T.L.2
-
5
-
-
11244279679
-
Relaxation matrix analysis of 2D NMR Data
-
Borgias, B. A., Gochin, M., Kerwood, D., and James, T. L. (1990) Relaxation Matrix Analysis of 2D NMR Data. Prog. NMR Spectrosc. 22, 83-100.
-
(1990)
Prog. NMR Spectrosc.
, vol.22
, pp. 83-100
-
-
Borgias, B.A.1
Gochin, M.2
Kerwood, D.3
James, T.L.4
-
6
-
-
84986513567
-
Determinating atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis
-
Breneman, C. M., and Wiberg, K. B. (1990) Determinating Atom-Centered Monopoles from Molecular Electrostatic Potentials. The Need for High Sampling Density in Formamide Conformational Analysis. J. Comput. Chem. 11, 361-373.
-
(1990)
J. Comput. Chem.
, vol.11
, pp. 361-373
-
-
Breneman, C.M.1
Wiberg, K.B.2
-
7
-
-
0033199558
-
On the sequence selective bis-intercalation of a Homodimeric Thiazole Orange Dye in DNA
-
In press
-
Bunkenborg, J., Stidsen, M. M., and Jacobsen, J. P. (1999) On the Sequence Selective Bis-intercalation of a Homodimeric Thiazole Orange Dye in DNA. Bioconjugate Chem. (In press).
-
(1999)
Bioconjugate Chem.
-
-
Bunkenborg, J.1
Stidsen, M.M.2
Jacobsen, J.P.3
-
8
-
-
0029011701
-
A second generation force field for the simulation of Proteins, Nucleic Acids, and Organic Molecules
-
Cornell, W. D., Cieplak, P., Bayly, I., Gould, I. R., Merz, K. M., Ferguson, D. M., Spellmeyer, D. C., Fox, T., Caldwell, J. W., and Kollman, P. A. (1995) A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
9
-
-
84986492501
-
Computer-assisted Pseudorotation Analysis of five-membered rings by means of Proton Spin-Spin coupling constants: Program PSEUROT
-
de Leeuw, F. A. A. M., and Altona, C. (1983) Computer-Assisted Pseudorotation Analysis of Five-Membered Rings by Means of Proton Spin-Spin Coupling Constants: Program PSEUROT. J. Comput. Chem 4, 428-437.
-
(1983)
J. Comput. Chem
, vol.4
, pp. 428-437
-
-
De Leeuw, F.A.A.M.1
Altona, C.2
-
10
-
-
0024454946
-
Definitions and nomenclature of Nucleic Acid structure parameters
-
Dickerson, R. E., Bansal, M., Calladine, C. R., Diekmann, S., Hunter, W. N., Kennard, O., von Kitzing, E., Nelson, H. C. M., Lavery, R., Olson, W. K., Saenger, W., Shakked, Z., Soumpasis, D. M., Tung, C.-S., Sklenar, H., Wang, A. H. J., and Zhurkin, V. B. (1989) Definitions and Nomenclature of Nucleic Acid Structure Parameters. EMBO J. 8, 1-4.
-
(1989)
EMBO J.
, vol.8
, pp. 1-4
-
-
Dickerson, R.E.1
Bansal, M.2
Calladine, C.R.3
Diekmann, S.4
Hunter, W.N.5
Kennard, O.6
Von Kitzing, E.7
Nelson, H.C.M.8
Lavery, R.9
Olson, W.K.10
Saenger, W.11
Shakked, Z.12
Soumpasis, D.M.13
Tung, C.-S.14
Sklenar, H.15
Wang, A.H.J.16
Zhurkin, V.B.17
-
11
-
-
0004133516
-
-
Rev D.3, Gaussian Inc, Pittsburgh, PA
-
Frisch, M. J., Trucks, G. W., Schlegel, H. B., Gill, P. M. W., Johnson, B. G., Robb, M. A., Cheeseman, J. R., Keith, T. A., Petersson, G. A., Montgomery, J. A., Raghavachari, K., Al-Laham, M. A., Zakrewski, V. G., Ortiz, J. V., Foresman, J. B., Cioslowski, J., Stefanov, B. B., Nanayakkara, A., Challacombe, M., Peng, C. Y., Ayala, P. Y., Chen, W., Wong, M. W., Andres, J. L., Replogle, E. S., Comperts, R., Martin, R. L., Fox, D. J., Binkley, J. S., Defrees, D. J., Baker, J., Stewart, J. P., Head-Gordon, M., Gonzalez, C., and Pople, J. A. (1995) Gaussian94 (Rev D.3), Gaussian Inc, Pittsburgh, PA.
-
(1995)
Gaussian94
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Gill, P.M.W.4
Johnson, B.G.5
Robb, M.A.6
Cheeseman, J.R.7
Keith, T.A.8
Petersson, G.A.9
Montgomery, J.A.10
Raghavachari, K.11
Al-Laham, M.A.12
Zakrewski, V.G.13
Ortiz, J.V.14
Foresman, J.B.15
Cioslowski, J.16
Stefanov, B.B.17
Nanayakkara, A.18
Challacombe, M.19
Peng, C.Y.20
Ayala, P.Y.21
Chen, W.22
Wong, M.W.23
Andres, J.L.24
Replogle, E.S.25
Comperts, R.26
Martin, R.L.27
Fox, D.J.28
Binkley, J.S.29
Defrees, D.J.30
Baker, J.31
Stewart, J.P.32
Head-Gordon, M.33
Gonzalez, C.34
Pople, J.A.35
more..
-
12
-
-
44949280676
-
Band-selective Radio frequency pulses
-
Geen, H., and Freeman, R. (1991) Band-Selective Radio frequency Pulses. J. Magn. Reson. 93, 93-141.
-
(1991)
J. Magn. Reson.
, vol.93
, pp. 93-141
-
-
Geen, H.1
Freeman, R.2
-
13
-
-
0027129003
-
Stable dye-DNA intercalation complexes as reagents for high-sensitivity fluorescence detection
-
Glazer, A. N., and Rye, H. S. (1992) Stable Dye-DNA Intercalation Complexes as Reagents for High-Sensitivity Fluorescence Detection. Nature 359, 859-861.
-
(1992)
Nature
, vol.359
, pp. 859-861
-
-
Glazer, A.N.1
Rye, H.S.2
-
15
-
-
0029864991
-
Bis-intercalation of a Homodimeric Thiazole Orange Dye in DNA in Symmetrical Pyrimidine-Pyrimidine-Purine-Purine oligonucleotides
-
Hansen, L. F., Jensen, L. K., and Jacobsen, J. P. (1996) Bis-Intercalation of a Homodimeric Thiazole Orange Dye in DNA in Symmetrical Pyrimidine-Pyrimidine-Purine-Purine oligonucleotides. Nucleic Acids Res. 24, 859-867.
-
(1996)
Nucleic Acids Res.
, vol.24
, pp. 859-867
-
-
Hansen, L.F.1
Jensen, L.K.2
Jacobsen, J.P.3
-
16
-
-
0028902956
-
Site selective bis-intercalation of a Homodimeric Thiazole Orange Dye in DNA Oligonucleotides
-
Jacobsen, J. P., Pedersen, J. B., Hansen, L. F., and Wemmer, D. E. (1995) Site Selective Bis-Intercalation of a Homodimeric Thiazole Orange Dye in DNA Oligonucleotides. Nucleic Acids Res. 23, 753-760.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 753-760
-
-
Jacobsen, J.P.1
Pedersen, J.B.2
Hansen, L.F.3
Wemmer, D.E.4
-
17
-
-
0000845385
-
Bis-intercalation of Homodimeric Thiazole Orange Dyes in selective binding sites of DNA studied by 1H NMR spectroscopy
-
Jensen, L. K., Gotfredsen, C. H., Bondensgaard, K., and Jacobsen, J. P. (1998) Bis-Intercalation of Homodimeric Thiazole Orange Dyes in Selective Binding Sites of DNA Studied by 1H NMR spectroscopy. Acta Chem. Scand. 52, 641-650.
-
(1998)
Acta Chem. Scand.
, vol.52
, pp. 641-650
-
-
Jensen, L.K.1
Gotfredsen, C.H.2
Bondensgaard, K.3
Jacobsen, J.P.4
-
18
-
-
0024058085
-
The definition af Generalized Helicoidal Parameters and for axis curvature of irregular Nucleic Acids
-
Lavery, R., and Sklenar, H. (1988) The Definition af Generalized Helicoidal Parameters and for Axis Curvature of Irregular Nucleic Acids. J. Biomol. Struct. Dyn. 6, 63-91.
-
(1988)
J. Biomol. Struct. Dyn.
, vol.6
, pp. 63-91
-
-
Lavery, R.1
Sklenar, H.2
-
19
-
-
0024539180
-
Defining the structure of irregular Nucleic Acids: Conventions and principles
-
Lavery, R., and Sklenar, H. (1989) Defining the Structure of Irregular Nucleic Acids: Conventions and Principles. J. Biomol. Struct. Dyn. 7, 655-667.
-
(1989)
J. Biomol. Struct. Dyn.
, vol.7
, pp. 655-667
-
-
Lavery, R.1
Sklenar, H.2
-
20
-
-
0029450044
-
Interproton distances bounds from 2D-NOE intensities: Effect of experimental noise and peak integration errors
-
Liu, H., Spielmann, H. P., Ulyanov, N. A., Wemmer, D. E., and James, T. L. (1995) Interproton Distances Bounds from 2D-NOE Intensities: Effect of Experimental Noise and Peak Integration Errors. J. Bio. NMR 6, 390-402.
-
(1995)
J. Bio. NMR
, vol.6
, pp. 390-402
-
-
Liu, H.1
Spielmann, H.P.2
Ulyanov, N.A.3
Wemmer, D.E.4
James, T.L.5
-
21
-
-
0001605673
-
Sugar conformation in intramolecular DNA triplexes determined by coupling constants obtained by automated simulation of P.Cosy cross peaks
-
Macaya, R. F., Schultze, P., and Feigon, J. (1992) Sugar Conformation in Intramolecular DNA Triplexes Determined by Coupling Constants Obtained by Automated Simulation of P.COSY Cross Peaks. J. Am. Chem. Soc. 114, 781-783.
-
(1992)
J. Am. Chem. Soc.
, vol.114
, pp. 781-783
-
-
Macaya, R.F.1
Schultze, P.2
Feigon, J.3
-
22
-
-
84986437005
-
Macromodel - An integrated software system for modeling organic and bioorganic molecules using molecular mechanics
-
Mohamadi, F., Richards, N. G. J., Guida, W. C., Liskamp, R., Lipton, M., Caufield, C., Chang, G., Hendrickson, T., and Still, W. C. (1990) MacroModel - An Integrated Software System for Modeling Organic and Bioorganic Molecules Using Molecular Mechanics. J. Comput. Chem 11, 440-452.
-
(1990)
J. Comput. Chem
, vol.11
, pp. 440-452
-
-
Mohamadi, F.1
Richards, N.G.J.2
Guida, W.C.3
Liskamp, R.4
Lipton, M.5
Caufield, C.6
Chang, G.7
Hendrickson, T.8
Still, W.C.9
-
23
-
-
0032079881
-
Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO modified on the Benzothiazole Ring
-
Petersen, M., and Jacobsen, J. P. (1998) Solution Structure of a DNA Complex with the Fluorescent Bis-Intercalator TOTO Modified on the Benzothiazole Ring. Bioconjugate Chem. 9, 331-340.
-
(1998)
Bioconjugate Chem.
, vol.9
, pp. 331-340
-
-
Petersen, M.1
Jacobsen, J.P.2
-
24
-
-
0004161838
-
-
Cambridge University Press, Cambridge
-
Press, W. H., Flannery, B. P., Teukolsky, S. A., and Vetterling, W. T. (1986) Numerical Recipes, Cambridge University Press, Cambridge.
-
(1986)
Numerical Recipes
-
-
Press, W.H.1
Flannery, B.P.2
Teukolsky, S.A.3
Vetterling, W.T.4
-
25
-
-
0026090666
-
High-sensitivity two-color detection of double-stranded DNA with a confocal fluorescence gel scanner using Ethidium Homodimer and Thiazole Orange
-
Rye, H. S., Quesada, M. A., Peck, K., Mathies, R. A., and Glazer, A. N. (1990) High-Sensitivity Two-Color Detection of Double-Stranded DNA with a Confocal Fluorescence Gel Scanner using Ethidium Homodimer and Thiazole Orange. Nucleic Acids Res. 19, 327-333.
-
(1990)
Nucleic Acids Res.
, vol.19
, pp. 327-333
-
-
Rye, H.S.1
Quesada, M.A.2
Peck, K.3
Mathies, R.A.4
Glazer, A.N.5
-
26
-
-
0026696234
-
Stable fluorescent complexes of double-stranded DNA with bis-Intervalating Asymmetric Cyanine Dyes: Properties and applications
-
Rye, H. S., Yue, S., Wemmer, D. E., Quesada, M. A., Haugland, R. P., Mathies, R. A., and Glazer, A. N. (1992) Stable Fluorescent Complexes of Double-stranded DNA with Bis-Intervalating Asymmetric Cyanine Dyes: Properties and Applications. Nucleic Acids Res. 20, 2803-2812.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 2803-2812
-
-
Rye, H.S.1
Yue, S.2
Wemmer, D.E.3
Quesada, M.A.4
Haugland, R.P.5
Mathies, R.A.6
Glazer, A.N.7
-
27
-
-
0027243117
-
Picogram detection of stable dye-DNA intercalation complexes with two-color laser-excited confocal fluorescence gel scanner
-
Rye, H. S., Yue, S., Quesada, M. A., Haugland, R. P., Mathies, R. A., and Glazer, A. N. (1993a) (30) Picogram Detection of Stable Dye-DNA Intercalation Complexes with Two-Color Laser-Excited Confocal Fluorescence Gel Scanner. Methods in Enzymology 217, 414-431.
-
(1993)
Methods in Enzymology
, vol.217
, Issue.30
, pp. 414-431
-
-
Rye, H.S.1
Yue, S.2
Quesada, M.A.3
Haugland, R.P.4
Mathies, R.A.5
Glazer, A.N.6
-
28
-
-
0027499414
-
Fluorometric assay using dimeric dyes for double- and single-stranded DNA and RNA with picogram sensitivity
-
Rye, H. S., Dabora, J. M., Quesada, M. A., Mathies, R. A., and Glazer, A. N. (1993b) Fluorometric Assay Using Dimeric Dyes for Double- and Single-Stranded DNA and RNA with Picogram Sensitivity. Anal. Biochem. 208, 144-150.
-
(1993)
Anal. Biochem.
, vol.208
, pp. 144-150
-
-
Rye, H.S.1
Dabora, J.M.2
Quesada, M.A.3
Mathies, R.A.4
Glazer, A.N.5
-
29
-
-
0345370890
-
-
Unpublished results
-
Spielmann, H. P. (1998a) Unpublished results.
-
(1998)
-
-
Spielmann, H.P.1
-
30
-
-
0032374093
-
13C NMR spectroscopy
-
13C NMR Spectroscopy. Biochemistry 37, 16863-16876.
-
(1998)
Biochemistry
, vol.37
, pp. 16863-16876
-
-
Spielmann, H.P.1
-
31
-
-
0029013864
-
Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy
-
Spielmann, H. P., Wemmer, D. E., and Jacobsen, J. P. (1995) Solution Structure of a DNA Complex with the Fluorescent Bis-Intercalator TOTO Determined by NMR Spectroscopy. Biochemistry 34, 8542-8553.
-
(1995)
Biochemistry
, vol.34
, pp. 8542-8553
-
-
Spielmann, H.P.1
Wemmer, D.E.2
Jacobsen, J.P.3
-
32
-
-
0031281272
-
Bis-intercalation of Homodimeric Thiazole Orange Dyes in DNA: The effect of modifying the linker
-
Stærk, D., Hamed, A. A., Pedersen, E. B., and Jacobsen, J. P. (1997) Bis-Intercalation of Homodimeric Thiazole Orange Dyes in DNA: The Effect of Modifying the Linker. Bioconjugate Chem. 8, 869-877.
-
(1997)
Bioconjugate Chem.
, vol.8
, pp. 869-877
-
-
Stærk, D.1
Hamed, A.A.2
Pedersen, E.B.3
Jacobsen, J.P.4
-
33
-
-
0344778061
-
Semianalytical treatment of solvation for molecular mechanics and dynamics
-
Still, W. C., Tempczyk, A., Hawley, R. C., and Hendrikson, T. (1990) Semianalytical Treatment of Solvation for Molecular Mechanics and Dynamics. J. Am. Chem. Soc. 112, 6127-6129.
-
(1990)
J. Am. Chem. Soc.
, vol.112
, pp. 6127-6129
-
-
Still, W.C.1
Tempczyk, A.2
Hawley, R.C.3
Hendrikson, T.4
-
34
-
-
0022445682
-
Polyfunctional DNA intercalating agents
-
Wakelin, L. P. G. (1986) Polyfunctional DNA intercalating agents. Med. Res. Rev. 6, 275-340.
-
(1986)
Med. Res. Rev.
, vol.6
, pp. 275-340
-
-
Wakelin, L.P.G.1
-
35
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner, S. J., Kollman, P. A., Case, D. A., Singh, U. C., Ghio, C., Algona, G., Profeta, S., and Weiner, P. (1984) A New Force Field for Molecular Mechanical Simulation of Nucleic Acids and Proteins. J. Am. Chem. Soc. 106, 765-784.
-
(1984)
J. Am. Chem. Soc.
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Algona, G.6
Profeta, S.7
Weiner, P.8
-
36
-
-
84988053694
-
An all atom force field for simulation of proteins and nucleic acids
-
Weiner, S. J., Kollman, P. A., Nguyen, C. H., and Case, D. A. (1986) An All Atom Force Field for Simulation of Proteins and Nucleic Acids. J. Compt. Chem 7, 230-252.
-
(1986)
J. Compt. Chem
, vol.7
, pp. 230-252
-
-
Weiner, S.J.1
Kollman, P.A.2
Nguyen, C.H.3
Case, D.A.4
|