3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

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Pushing the limits of what is achievable in protein–DNA docking: benchmarking HADDOCK’s performance (2010, methodology): “The DNA structures in these solutions were analyzed using 3DNA (34,35) and the DNA bend analysis algorithm used in the 3D-DART server (29).”
Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures (2009, methodology): “5 Å—identify both canonical and non-canonical nucleotides interactions (1,2,14), e.”
DSSR: an integrated software tool for dissecting the spatial structure of RNA (2015, methodology): “These two programs are a defining feature of 3DNA (Lu and Olson, 2003, 2008; Li et al., 2019).”
Origins of specificity in protein-DNA recognition (2010, neutral): “To optimize both types of interactions, DNA structures vary with respect to three rotational parameters: roll (the relative rotation between adjacent base pairs with respect to the base pairing axis), helix twist (the relative rotation between adjacent base pairs with respect to the helix axis), and”
Making the Bend: DNA Tertiary Structure and Protein-DNA Interactions (2014, methodology): “Z-DNA with the sequence (GC)8 was constructed with 3DNA [14].”
Conformational analysis of nucleic acids revisited: Curves+ (2009, methodology): “This is the approach adopted by 3DNA (14,15), which is now one of the commonly used analysis programs.”