Insight II

A       References

The following are explicitly referenced in the Insight II program's printed or online documentation.

Arnott, S. and Hukins, D. W. L. "Optimised Parameters for A-DNA B-DNA" Biochem. Biophys. Res. Comm., 47, 1504-1509 (1972).

Arnott, S.; Hukins, D. W. L.; and Dover, S. D. "Optimised Parameters for RNA Double Helices" Biochem. Biophys. Res. Comm., 48, 1392-1399 (1972).

Arnott, S. and Selsing, E.; "Structures for the Polynucleotide Complexes
Poly(dA).Poly(dT) and Poly(dT).Poly(dA).Poly(dT)" J. Molec. Biol., 88, 509-521 (1974).

Baker, J. "An algorithm for the location of transition states", J. Comp. Chem., 7, 385 (1986).

Baker, J. "Geometry optimization in Cartesian coordinates: Constrained optimization", J. Comp. Chem., 13, 240 (1992).

Baker, J. "Techniques for geometry optimization: A comparison of Cartesian and natural internal coordinates", J. Comp. Chem., 14, 1085 (1993).

Baker, J.; Bergeron, D. "Constrained optimization in Cartesian coordinates", J. Comp. Chem., 14, 1339 (1993).

Baker, J.; Hehre, W. J. "Geometry optimization in Cartesian coordinates: The end of the Z-matrix?", J. Comp. Chem., 12, 606 (1991).

Banerjee, A.; Adams, N.; Simons, J.; Shepard, R. "Search for stationary points on surfaces", J. Phys. Chem., 89, 52 (1985).

Besler, B. H.; Merz, K. M.; and Kollman, P.A. "Atomic Charges Derived Semiempirical Methods" J. Comp. Chem Vol. 11, No. 4, 431-439 (1990).

Bracewell, R. N. "Numerical Transforms", Science, 248, 679 (1990).

Császár, P.; Pulay, P. "Geometry optimization by direct inversion in the iterative subspace", J. Mol. Struct., 114, 31-34 (1984).

Fletcher, R. Practical Methods of Optimization, Vol. 2, Constrained Optimization, John Wiley & Sons: New York (1981).

Fogarasi, G.; Zhou, X.; Taylor, P. W.; Pulay, P. "The calculation of ab initio molecular geometries: Efficient optimization by natural internal coordinates", J. Amer. Chem. Soc., 114, 8191 (1992).

Hagler, A. T.; Osguthorpe, D. J.; Dauber-Osguthorpe, P.; and Hemple, J. C. "Dynamics and Conformational Energetics of a Peptide Hormone: Vasopressin", Science 227, 1309-1315 (1985).

Hagler, A. T. and Moult, J. "Computer Simulation of the Solvent Structure Around Biological Macromolecules", Nature 272, 222-226 (1978).

Hagler, A. T.; Lifson, S.; and Dauber, P. "Consistent Force Field Studies of Intermolecular Forces in Hydrogen Bonded Crystals. II. A Benchmark for the Objective Comparison of Alternative Force Fields", J. Amer. Chem. Soc. 101, 5122-5130 (1979a).

Hagler, A. T.; Dauber, P.; and Lifson, S. "Consistent Force Field Studies of Intermolecular Forces in Hydrogen Bonded Crystals. III. The C=O...H-O Hydrogen Bond and the Analysis of the Energetics and Packing of Carboxylic Acids", J. Amer. Chem. Soc. 101, 5131-5141 (1979b).

Hagler, A. T.; Stern, P. S.; Sharon, R.; Becker, J. M.; and Naider, F. "Computer Simulation of the Conformational Properties of Oligopeptides. Comparison of Theoretical Methods and Analysis of Experimental Results", J. Amer. Chem. Soc. 101, 6842-6852 (1979c).

Hoyland, J.R.; "MINDO/2 Calculations on the Reaction of Methyl Radicals with Ethylene and Butadiene", Theor. Chim. Acta 22, 229-233 (1971).

Pattabiraman, N.; Levitt, M.; Ferrin, T. E.; and Langridge, R. "Computer Graphics in Real-time Docking with Energy Calculation and Minimization", J. Comp. Chem., 6, 432-436 (1985).

Press, W. H.; Flannery, B. P.; Teukolsky, S. A.; and Vetterling, W. T. in Numerical Recipes, The Art of Scientific Computing; Cambridge: Cambridge University Press, (1986).

Pulay, P., "Improved SCF convergence acceleration", J. Comp. Chem., 3, 556 (1982).

Saenger, W. in Principles of Nucleic Acid Structures; New York: Springer-Verlag, (1984).

Sessions, R. B.; Dauber-Osguthorpe, P.; and Dauber-Osguthorpe, D. J. "Filtering Molecular Dynamics Trajectories to Reveal Low Frequency Collective Motions: Phospholipase A2", J. Molec. Biol., 210, 617 (1989).

Watson, J. D. in Molecular Biology of the Gene; Menlo Park, CA: W. A. Benjamin, Inc., (1976).

Last updated December 17, 1998 at 04:28PM PST.
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