VDNA: The virtual DNA plug-in for VMD

Bioinformatics

Volumn 25, Issue 23, 2009, Pages 3187-3188

  Bishop, Thomas C ^a  

^a TULANE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARTICLE; BINDING SITE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; METABOLISM; METHODOLOGY; STRUCTURE ACTIVITY RELATION;

BINDING SITES; COMPUTATIONAL BIOLOGY; DNA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 75949110439     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp566     Document Type: Article

References (10)

1. Bishop, T.C. (2008) Geometry of the nucleosomal DNA superhelix. Biophys J., 95, 1007-1017.
2. Dickerson, R.E. (1989) Definitions and nomenclature of nucleic acid structure components. Nucleic Acids Res., 17, 1797-1803.
3. El Hassan, M.A. and Calladine, C.R. (1995) The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme. J. Mol. Biol., 251, 648-664.
4. Humphrey, W. et al. (1996) VMD: visual molecular dynamics. J. Mol. Graph., 14, 33-38, 27-28.
5. Lavery, R. and Sklenar, H. (1988) The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. J. Biomol. Struct. Dyn., 6, 63-91.
6. Lavery, R. et al. (2009) A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic Acids Res., [Epub ahead of print, doi:10.1093/nar/gkp834, October 22, 2009].
7. Lu, X.-J. and Olson, W.K. (2003) 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. Nucleic Acids Res., 31, 5108-5121.
8. Macke, T. and Case, D.A (1998) Modeling unusual nucleic acid structures. In Leontes, N.B. and SantaLucia, J. Jr., eds. Molecular Modeling of Nucleic Acids, American Chemical Society, Washington, DC, pp. 379-393.
9. Tung, C S. and Carter, E.S. (1994) Nucleic acid modeling tool (NAMOT): an interactive graphic tool for modeling nucleic acid structures. Comput. Appl. Biosci., 10, 427-433.
10. Vlahovicek, K. and Pongor, S. (2000) Model.it: building three dimensional DNA models from sequence data. Bioinformatics, 16, 1044-1045.