A standard reference frame for the description of nucleic acid base-pair geometry.

By Wilma K. Olson, M. Bansal, Stephen K. Burley, R. Dickerson, Mark Gerstein, S. Harvey, U. Heinemann, X. J. Lu, Stephen Neidle, Z. Shakked and 6 more. Journal of Molecular Biology, 2001

576 citations recorded by the source corpus.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/57dce8e5f4df9a208ce7bf829bb279fe7b7a9a78

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Citations in the corpus

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures (2008, background): “The arrangements of paired bases are defined with respect to the orientation and displacement of an ideal, planar Watson–Crick base pai”
3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures. (2003, methodology): “A 1988 workshop established conceptual guidelines for specifying the orientation and displacement of complementary bases and successive base pairs in double helical structures (19), and a standard base-centered reference frame was recently recommended for use in nucleic acid structural studies (20).”
DSSR: an integrated software tool for dissecting the spatial structure of RNA (2015, methodology): “(B) Bases are assigned a standard reference frame (Olson et al., 2001) that is independent of sequence identity: purines and pyrimidines are symmetrically placed with respect to the sugar.”
Long Range Interactions in Nanoscale Science. (2010, result): “By comparing the results with analyses Olson et al., 2001 of high-resolution crystalline data from the nucleic acid database, they imply that on a broad scale the answer to this question is yes.”
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures (2007, methodology): “First, we do not use the axis system of [2,40], which includes parameters such as buckle, propeller twist, opening, shear,”
Validation of the 53A6 GROMOS force field (2005, methodology): “Structural analyses of DNA base pair geometries were performed according to the rules as implemented in the 3DNA program (Lu and Olson 2003; Olson et al. 2001).”
Web 3DNA 2.0 for the analysis, visualization, and modeling of 3D nucleic acid structures (2019, methodology): “of the phosphorus atoms (P) and the origins of the intervening bases in their standard base reference frames (7).”
Tools for the automatic identification and classification of RNA base pairs (2003, methodology): “A standard reference frame is used for base pair determination (11).”
Conformational analysis of nucleic acids revisited: Curves+ (2009, background): “The choice of base reference system is that established at the Tsukuba meeting (13).”
Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures (2009, methodology): “The set of parameters and the coordinate frames used in the 3DNA software follow established, community-developed guidelines (10,11).”