A Standard Reference Frame for the Description
of Nucleic Acid Base-pair Geometry
Supplementary Material

List of Programs and References

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1. CEHS
   • M. A. El Hassan & C. R. Calladine (1995). ``The Assessment of the Geometry of Dinucleotide Steps in Double-Helical DNA: A New Local Calculation Scheme.'' J. Mol. Biol. 251, 648-664.
   • X. J. Lu, M. A. El Hassan & C. A. Hunter (1997). ``Structure and Conformation of Helical Nucleic Acids: Analysis Program (SCHNAaP).'' J. Mol. Biol. 273, 668-680.

2. CompDNA (Please refer to Dr. Andrey A. Gorin: agor@sbnmr1.ski.mskcc.org OR Dr. Victor B. Zhurkin: zhurkin@lmmb.nci.nih.gov)
   • A. A. Gorin, V. B. Zhurkin & W. K. Olson (1995). ``B-DNA Twisting Correlates with Base-pair Morphology.'' J. Mol. Biol. 247, 34-48.
   • K. M. Kosikov, A. A. Gorin, V. B. Zhurkin & W. K. Olson (1999). ``DNA Stretching and Compression: Large-scale Simulations of Double Helical Structures." J. Mol. Biol. 289, 1301-1326.

3. Curves (Please refer to Prof. Richard Lavery: richard@ibpc.fr)
   • R. Lavery & H. Sklenar (1988). ``The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids.'' J. Biomol. Struct. Dynam. 6, 63-91.
   • R. Lavery & H. Sklenar (1989). ``Defining the Structure of Irregular Nucleic Acids: Conventions and Principles.'' J. Biomol. Struct. Dynam. 6, 655-667.

4. FREEHELIX
   • R. E. Dickerson (1998). ``DNA Bending: The Prevalence of Kinkiness and the Virtues of Normality.'' Nucl. Acids Res. 26, 1906-1926.

5. NGEOM (Please refer to Dr. Chang-Shung Tung: cst@t10.lanl.gov)
   • D. M. Soumpasis & C. S. Tung (1988). ``A Rigorous Basepair Oriented Description of DNA Structures.'' J. Biomol. Struct. Dynam. 6, 397-420.
   • C. S. Tung, D. M. Soumpasis & G. Hummer (1994). ``An Extension of the Rigorous Base-Unit Oriented Description of Nucleic-Acid Structures.'' J. Biomol. Struct. Dynam. 11, 1327-1344.

6. NUPARM (Please refer to Prof. Manju Bansal: mb@mbu.iisc.ernet.in)
   • D. Bhattacharyya & M. Bansal (1989). ``A Self-Consistent Formulation for Analysis and Generation of Non-Uniform DNA Structures.'' J. Biomol. Struct. Dynam. 6, 635-653.
   • M. Bansal, D. Bhattacharyya & B. Ravi (1995). ``NUPARM and NUCGEN: Software for Analysis and Generation of Sequence Dependent Nucleic Acid Structures.'' Comput. Appl. Biosci. 11, 281-287.

7. RNA
   • M. S. Babcock & W. K. Olson (1994). ``The Effect of Mathematics and Coordinate System on Comparability and `Dependencies' of Nucleic Acid Structure Parameters.'' J. Mol. Biol.. 237, 98-124.
   • M. S. Babcock, E. P. D. Pednault & W. K. Olson (1994). ``Nucleic Acid Structure Analysis: Mathematics for Local Cartesian and Helical Structure Parameters That Are Truly Comparable Between Structures.'' J. Mol. Biol. 237, 125-156.
   • E. P. D. Pednault, M. S. Babcock & W. K. Olson (1993). ``Nucleic Acids Structure Analysis: A Users Guide to a Collection of New Analysis Programs.'' J. Biomol. Struct. Dynam.. 11, 597-628.

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Web page created by Dr. Xiang-Jun Lu <http://rutchem.rutgers.edu/~xiangjun/>

Last modified: Fri Apr 7 18:52:38 2000