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w3DNA - web 3DNA Interface

w3DNA (web 3DNA) is a user-friendly web-based interface to the 3DNA software package for the analysis, reconstruction, and visualization of three-dimensional nucleic acid-containing structures, including their complexes with proteins and other ligands. Although this versatile and integrated suite of programs is widely used in the scientific community, its command-line-driven style is not especially user-friendly, for either novices (non-Linux/Unix users) or educational purposes.

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w3DNA - web 3DNA Interface | w3dna.rutgers.edu Reviews
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w3DNA (web 3DNA) is a user-friendly web-based interface to the 3DNA software package for the analysis, reconstruction, and visualization of three-dimensional nucleic acid-containing structures, including their complexes with proteins and other ligands. Although this versatile and integrated suite of programs is widely used in the scientific community, its command-line-driven style is not especially user-friendly, for either novices (non-Linux/Unix users) or educational purposes.
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w3DNA - web 3DNA Interface | w3dna.rutgers.edu Reviews

https://w3dna.rutgers.edu

w3DNA (web 3DNA) is a user-friendly web-based interface to the 3DNA software package for the analysis, reconstruction, and visualization of three-dimensional nucleic acid-containing structures, including their complexes with proteins and other ligands. Although this versatile and integrated suite of programs is widely used in the scientific community, its command-line-driven style is not especially user-friendly, for either novices (non-Linux/Unix users) or educational purposes.

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w3dna.rutgers.edu w3dna.rutgers.edu
1

w3DNA - web 3DNA Interface

http://w3dna.rutgers.edu/index.php/doc/tutorial

Web 3DNA for analysis, reconstruction and visualization of nucleic-acid structures. Monday, September 05, 2016 03:08. Analysis by PDB/NDB ID. For a nucleic-acid-containing structure deposited in the Protein Data Bank (PDB) or Nucleic Acid Database (NDB), one can directly type in the valid ID. Before, conducting an analysis on the website, users are encouraged to verify the PDB/NDB ID at the PDB or NDB website and gain some familiarity with the structure. Example 1 -1: Type in a PDB ID 1HRZ. Taking the lo...

2

w3DNA - web 3DNA Interface

http://w3dna.rutgers.edu/index.php/rebuild

Web 3DNA for analysis, reconstruction and visualization of nucleic-acid structures. Monday, September 05, 2016 03:08. Choose a DNA fiber. B-DNA (generic alternate) (BI-type nucleotides). C-DNA (generic alternate) (BII-type nucleotides). C-DNA (generic alternate) (left-handed). A-DNA poly d(ABr5U) : poly d(ABr5U). A-DNA poly d(A1T2C3G4G5A6A7T8G9G10T11) : poly d(A. B-DNA poly d(CG) : poly d(CG). B-DNA poly d(C1C2C3C4C5) : poly d(G6G7G8G9G10). B-DNA poly d(A) : poly d(T) (Ca salt). DNA-RNA hybrid poly (A) :...

3

w3DNA - web 3DNA Interface

http://w3dna.rutgers.edu/index.php/visualize

Web 3DNA for analysis, reconstruction and visualization of nucleic-acid structures. Monday, September 05, 2016 03:07. Choose a visualization type. Block representation of a pdb structure. Stacking diagram of base-pair steps. Block representation of an ensemble of structures. 2008-2009 Guohui Zheng@Dr. Wilma K. Olson Group, Rutgers, the State University of New Jersey. New Brunswick, New Jersey, USA.

4

w3DNA - web 3DNA Interface

http://w3dna.rutgers.edu/index.php/doc/citation

Web 3DNA for analysis, reconstruction and visualization of nucleic-acid structures. Monday, September 05, 2016 03:07. When using w3DNA, please cite:. Zheng G., Lu X-J. and Olson W.K. (2009) Web 3DNA a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures, Nucleic Acids Research 37(Web Server issue), W240-W246. More desciption regarding 3DNA, please cite:. New Brunswick, New Jersey, USA.

5

w3DNA - web 3DNA Interface

http://w3dna.rutgers.edu/index.php/doc/about

Web 3DNA for analysis, reconstruction and visualization of nucleic-acid structures. Monday, September 05, 2016 03:07. Our new web-based interface provides straightforward access to some of the most popular features of the software, including:. The visualization component creates vector-based drawings and scenes that can be rendered as raster-graphics images, allowing for easy generation of publication-quality figures. The server takes a user-uploaded PDB file or a PDB/NDB ID, and returns various repr...

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home.x3dna.org home.x3dna.org

3DNA Homepage -- Nucleic Acid Structures

http://home.x3dna.org/highlights/pauling-triplex-model-of-nucleic-acids-is-available-in-3dna

3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. Highlights of recent developments of 3DNA/DSSR. Rsaquo; Paulings triplex model of nucleic acids is available in 3DNA. 3DNA C source code is available. The DSSR - block-color option. Integrating DSSR into Jmol and PyMOL. Characterization of base-pair geometry. DSSR base blocks in PyMOL, interactively. Details on the simple base-pair parameters. Fitting of base reference frame. In a r...

home.x3dna.org home.x3dna.org

3DNA Homepage -- Nucleic Acid Structures

http://home.x3dna.org/highlights/the-dssr-block-color-option

3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. Highlights of recent developments of 3DNA/DSSR. Paulings triplex model of nucleic acids is available in 3DNA. 3DNA C source code is available. Rsaquo; The DSSR - block-color option. Integrating DSSR into Jmol and PyMOL. Characterization of base-pair geometry. DSSR base blocks in PyMOL, interactively. Details on the simple base-pair parameters. Fitting of base reference frame. Script...

home.x3dna.org home.x3dna.org

3DNA Homepage -- Nucleic Acid Structures

http://home.x3dna.org/articles/cartoon-block-representation-of-quadruplex-duplex-interface

3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. PyMOL wrapper to 3DNA fiber models. Rsaquo; Cartoon-block representation of quadruplex-duplex interface. 3DNA Forum is spam free. Ask reproducible questions, publicly. Simple parameters for non-Watson-Crick base pairs. Quality control of DSSR (3DNA) source code. Metallo-base pairs can be identified by DSSR. Middot; Weird PDB entries. Middot; 3DNA fiber models. I quickly ran DSSR.

home.x3dna.org home.x3dna.org

3DNA Homepage -- Nucleic Acid Structures

http://home.x3dna.org/articles/3dna-fiber-models

3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. Rsaquo; 3DNA fiber models. PyMOL wrapper to 3DNA fiber models. Cartoon-block representation of quadruplex-duplex interface. 3DNA Forum is spam free. Ask reproducible questions, publicly. Simple parameters for non-Watson-Crick base pairs. Quality control of DSSR (3DNA) source code. Metallo-base pairs can be identified by DSSR. Middot; Weird PDB entries. Middot; 3DNA fiber models.

home.x3dna.org home.x3dna.org

3DNA Homepage -- Nucleic Acid Structures

http://home.x3dna.org/highlights/highlights-of-recent-developments-of-3dna-dssr

3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. Rsaquo; Highlights of recent developments of 3DNA/DSSR. Paulings triplex model of nucleic acids is available in 3DNA. 3DNA C source code is available. The DSSR - block-color option. Integrating DSSR into Jmol and PyMOL. Characterization of base-pair geometry. DSSR base blocks in PyMOL, interactively. Details on the simple base-pair parameters. Fitting of base reference frame. Subdir...

home.x3dna.org home.x3dna.org

3DNA Homepage -- Nucleic Acid Structures

http://home.x3dna.org/highlights/dssr-base-blocks-in-pymol-interactively

3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. Highlights of recent developments of 3DNA/DSSR. Paulings triplex model of nucleic acids is available in 3DNA. 3DNA C source code is available. The DSSR - block-color option. Integrating DSSR into Jmol and PyMOL. Characterization of base-pair geometry. Rsaquo; DSSR base blocks in PyMOL, interactively. Details on the simple base-pair parameters. Fitting of base reference frame. 8217;s...

home.x3dna.org home.x3dna.org

3DNA Homepage -- Nucleic Acid Structures

http://home.x3dna.org/articles/outside-links

3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. PyMOL wrapper to 3DNA fiber models. Cartoon-block representation of quadruplex-duplex interface. 3DNA Forum is spam free. Ask reproducible questions, publicly. Simple parameters for non-Watson-Crick base pairs. Quality control of DSSR (3DNA) source code. Metallo-base pairs can be identified by DSSR. Middot; Weird PDB entries. Middot; Highlights of recent developments of 3DNA/DSSR.

home.x3dna.org home.x3dna.org

3DNA Homepage -- Nucleic Acid Structures

http://home.x3dna.org/highlights/schematic-diagrams-of-base-pair-parameters

3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. Highlights of recent developments of 3DNA/DSSR. Paulings triplex model of nucleic acids is available in 3DNA. 3DNA C source code is available. The DSSR - block-color option. Integrating DSSR into Jmol and PyMOL. Characterization of base-pair geometry. DSSR base blocks in PyMOL, interactively. Details on the simple base-pair parameters. Fitting of base reference frame. Pictorial defi...

home.x3dna.org home.x3dna.org

3DNA Homepage -- Nucleic Acid Structures

http://home.x3dna.org/highlights/3dna-c-source-code-is-available

3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. Highlights of recent developments of 3DNA/DSSR. Paulings triplex model of nucleic acids is available in 3DNA. Rsaquo; 3DNA C source code is available. The DSSR - block-color option. Integrating DSSR into Jmol and PyMOL. Characterization of base-pair geometry. DSSR base blocks in PyMOL, interactively. Details on the simple base-pair parameters. Fitting of base reference frame. Compil...

home.x3dna.org home.x3dna.org

3DNA Homepage -- Nucleic Acid Structures

http://home.x3dna.org/articles/pymol-wrapper-to-3dna-fiber-models

3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. Rsaquo; PyMOL wrapper to 3DNA fiber models. Cartoon-block representation of quadruplex-duplex interface. 3DNA Forum is spam free. Ask reproducible questions, publicly. Simple parameters for non-Watson-Crick base pairs. Quality control of DSSR (3DNA) source code. Metallo-base pairs can be identified by DSSR. Middot; Weird PDB entries. Middot; 3DNA fiber models. Gives the following de...

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w3DNA - web 3DNA Interface

Web 3DNA for analysis, reconstruction and visualization of nucleic-acid structures. Saturday, August 15, 2015 12:38. Enter a PDB/NDB ID. Upload a PDB file. 2008-2009 Guohui Zheng@Dr. Wilma K. Olson Group, Rutgers, the State University of New Jersey. New Brunswick, New Jersey, USA.

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