3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.

By Xiang-Jun Lu, Wilma K. Olson. 2003

1,627 citations recorded by the source corpus.

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Citations in the corpus

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).”
A protein–DNA docking benchmark (2008, methodology): “Models for unbound DNA were generated using the DNA analysis and rebuilding program 3DNA (9) with the”
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.”
An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling (2011, methodology): “The canonical base pairs at the edges of the motif were assumed to be known a priori (2) and were built using idealized geometry (12).”
DSSR: an integrated software tool for dissecting the spatial structure of RNA (2015, methodology): “If the isolated pairs and pseudoknotted stem are not taken into account, the structure appears to form a [6,1,8,3] four-way junction loop as originally reported (48).”
Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility (2006, methodology): “Values for base pair and base pair step parameters as well as torsion angles for the sugarphosphate backbone and the sugar pucker were obtained using the program 3DNA (28).”
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures (2008, methodology): “Software overview 3DNA is a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid-containing structures, including their complexes with proteins and other ligand”
3D-DART: a DNA structure modelling server (2009, methodology): “However, most of these software packages, some of which are available via web-servers (4,7), are only able to generate models in ideal canonical conformations (5,7) or in conformations mimicking that of a free unbound structure (4).”
RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools (2019, methodology): “The interactions of an RNA structure can be extracted by programs such as MC-Annotate (25) and 3DNA (64).”
Three-dimensional EM structure of an intact activator-dependent transcription initiation complex (2009, methodology): “DNA from the fitted composite model was extended downstream by 5 ideal B-DNA base pairs; tilt, roll, twist, and rise parameters for positions 36 to 23 were manually adjusted using 3DNA (50) to produce a smooth bend of 15° and yield superimposed 23 bp positions for the two DNA model segments.”
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.”
A Left-Handed RNA Double Helix Bound by the Zα Domain of the RNA-Editing Enzyme ADAR1 (2007, methodology): “Analysis of the RNA conformation was performed with 3DNA (Lu and Olson, 2003).”