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3DNA specifications

Information


Unique identifier OMICS_14089
Name 3DNA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 2.3
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Xiang-Jun Lu <>

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Publication for 3DNA

3DNA in publications

 (79)
PMCID: 5871717
PMID: 29551265
DOI: 10.1016/j.cell.2018.02.032

[…] with pymol (schrödinger); sequence alignments were generated with dali () and espript (). protein interfaces were analyzed in pisa (), protein-dna contacts in nucplot () and dna parameters in 3dna ()., reaction products from strand exchange assays with int82n, r153a, and r153a-y160a mutants were quantified using a typhoon fla7000 phosphorimager and the imagequant tl software (ge […]

PMCID: 5814798
PMID: 29267876
DOI: 10.1093/nar/gkx1262

[…] 2.2.2 package () for a complementary cg modeling of the hc-system. the simulation parameters used are given in the ., the starting coordinates of the component dna helices were obtained with the 3dna v.2.3 software package (). the helices were arranged in 3d with the inter-strand distance of 24 å and, in case of the hc-system, angle of 240° using pymol molecular graphics system, v. 1.8.6.0 […]

PMCID: 5514533
PMID: 28715997
DOI: 10.1186/s12859-017-1755-0

[…] from tf dimers or tetramers. as shown in fig. , our previous prediction algorithm first generates tf-dna complexes consisting of a tf and every possible permutation of its target sequence using 3dna [, ]. the ie function is then applied to each tf-dna complex to calculate their binding energy and subsequently predict their binding sites (fig. ) []. the total number of tf-dna complex energy […]

PMCID: 5737332
PMID: 28637278
DOI: 10.1093/nar/gkx521

[…] completeness of 92.54%. four magnesium ions were detected. solution coordinates have been deposited in the protein data bank as pdb-id: 5lit. the dna structural parameters were calculated using the 3dna software (). drawings were prepared with pymol (http://www.pymol.org) and ccp4mg ()., the 5’-biotin labelled dna hairpins were purchased from sigma-aldrich with reverse-phase hplc purification. […]

PMCID: 5570162
PMID: 28472503
DOI: 10.1093/nar/gkx365

[…] program written in ansi c (). the single-file dssr binary executable is tiny (∼1mb) and self-contained (with zero dependencies), with an efficient and robust performance. dssr is a component of the 3dna suite of programs (,) for the analysis, rebuilding, and visualization of 3d nucleic acid structures. it has been designed to streamline the analysis and annotation of rna tertiary structures […]


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3DNA institution(s)
Department of Chemistry and Chemical Biology, Wright-Rieman Laboratories, The State University of New Jersey, Piscataway, NJ, USA
3DNA funding source(s)
This work has been supported by the US Public Health Service under research grant GM20861.

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