CURVES (R. Lavery)
Lavery R, Sklenar HJ. 1988. J Biomol Struct
Dyn. The
definition of generalized helicoidal parameters and of axis curvature
for irregular nucleic acids. J Biomol Struct Dyn, 6:
63-91.
Stofer E, Lavery R. 1994. Measuring the geometry of DNA grooves. Biopolymers, 34: 337-346.
FREEHELIX98
(R.E. Dickerson)
Dickerson RE, Chiu TK. 1997. Helix
bending as a factor in protein/DNA recognition. Biopolymers,
44: 361-403.
Dickerson RE. 1998. DNA bending: The prevalence of kinkiness and the virtues of normality. Nucleic Acids Res, 26: 1906-1926.
RASMOL
(R. Sayle)
Sayle RA, Milner-White EJ. 1995. RASMOL:
Biomolecular graphics for all. Trends Biochem Sci, 20: 374.
MOLSCRIPT (P. Kraulis)
Kraulis PJ. 1991. MOLSCRIPT: A program to produce
both detailed and schematic plots of protein structures. J Appl
Crystallogr, 23: 946-950.
RASTER3D
(E. A. Merritt)
Merritt EA, Bacon DJ. 1997. Raster3D:
Photorealistic Molecular Graphics. Methods Enzymol, 277: 505-524.
CHIRALITY (P. Slickers)
Checks chirality of ribose and phosphate atoms.
ARC_FIT (P. Slickers)
Fits straight line, plane, arc, kinked line,
double kinked line to a curved line in 3-dimensional space.
The program used here is an extension of the
program described in:
Slickers P, Hillebrand M, Kittler L, Lober G,
Suhnel J. Molecular
modelling and footprinting studies of DNA minor groove binders:
bisquaternary ammonium heterocyclic compounds. Anticancer Drug Des.
1998 Jul;13(5):463-88.
Nucleic acid structure
IUPAC-IUB Commission on Biochemical Nomenclature.
1970. Abbreviations
and symbols for nucleic acids, polynucleotides and their constituents.
Biochem J, 120: 449-454.
Dickerson RE. 1989. Definitions and nomenclature of nucleic acid structure components. Nucleic Acids Res, 17: 177-199.
Last modified: 14 August 2006
Author: Peter Slickers (jsuehnel@fli-leibniz.de)