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3DNA Homepage -- Nucleic Acid StructuresHomepage of the 3DNA suite of software programs for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures
http://home.x3dna.org/
Homepage of the 3DNA suite of software programs for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures
http://home.x3dna.org/
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3DNA Homepage -- Nucleic Acid Structures | home.x3dna.org Reviews
https://home.x3dna.org
Homepage of the 3DNA suite of software programs for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures
home.x3dna.org
3DNA Homepage -- Nucleic Acid Structures
http://home.x3dna.org/articles/seeing-is-understanding-as-well-as-believing
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.
3DNA Homepage -- Nucleic Acid Structures
http://home.x3dna.org/highlights
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. Subdirectory) ...
3DNA Homepage -- Nucleic Acid Structures
http://home.x3dna.org/highlights/blocview-a-simple-effective-visualization-tool-for-dna-rna-structures
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. And blue for T.
3DNA Homepage -- Nucleic Acid Structures
http://home.x3dna.org/articles
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.
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...
TOTAL PAGES IN THIS WEBSITE
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DNA-protein interactions (SNAP)
http://forum.x3dna.org/dna-protein-interactions
Q&As related to 3DNA. An online community for DNA/RNA structural bioinformatics 3DNA. DSSR v1.6.1-2016aug22: an integrated software tool for Dissecting the Spatial Structure of RNA, with web/Jmol/PyMOL interfaces and a user manual! SNAP: software for characterizing DNA-protein interactions. May 05, 2014, 01:22:59 am. May 21, 2016, 02:27:37 pm. Detection of stacking interactions. October 23, 2015, 12:01:46 am. Interaction code and other issues. July 28, 2015, 01:43:16 pm. Web version of SNAP?
DSSR-NAR paper
http://forum.x3dna.org/dssr-nar-paper
Q&As related to 3DNA. An online community for DNA/RNA structural bioinformatics 3DNA. DSSR v1.6.1-2016aug22: an integrated software tool for Dissecting the Spatial Structure of RNA, with web/Jmol/PyMOL interfaces and a user manual! Reproducing results published in the DSSR-NAR paper. July 03, 2015, 11:37:23 am. May 03, 2016, 11:01:31 am. RNA cartoon-block representations with PyMOL and DSSR. July 24, 2015, 02:18:56 pm. Figure 6 - analysis of the CRISPR Cas9-sgRNA-DNA ternary complex (4oo8). Supplementary...
interaction code and other issues
http://forum.x3dna.org/dna-protein-interactions/interaction-code-and-other-issues/msg1933
Q&As related to 3DNA. An online community for DNA/RNA structural bioinformatics 3DNA. DSSR v1.6.1-2016aug22: an integrated software tool for Dissecting the Spatial Structure of RNA, with web/Jmol/PyMOL interfaces and a user manual! Interaction code and other issues. Topic: interaction code and other issues (Read 3045 times). Interaction code and other issues. June 01, 2014, 04:13:25 pm. Really great work, thanks. Just a few remarks:. Why didn't you use the same nomenclature as in dssr? 171; Reply #1 on:.
w3DNA -- web interface to 3DNA
http://forum.x3dna.org/web-3dna
Q&As related to 3DNA. An online community for DNA/RNA structural bioinformatics 3DNA. DSSR v1.6.1-2016aug22: an integrated software tool for Dissecting the Spatial Structure of RNA, with web/Jmol/PyMOL interfaces and a user manual! W3DNA - web interface to 3DNA. Web-3DNA not running on some pdb entries. July 11, 2016, 11:35:21 am. W3DNA hanging on some structures. May 17, 2016, 03:39:58 am. MOVED: 3DNA can recognise DNA with S atoms? September 24, 2015, 11:31:04 pm. September 10, 2015, 03:36:27 pm. Creat...
RNA structures (DSSR)
http://forum.x3dna.org/rna-structures
Q&As related to 3DNA. An online community for DNA/RNA structural bioinformatics 3DNA. DSSR v1.6.1-2016aug22: an integrated software tool for Dissecting the Spatial Structure of RNA, with web/Jmol/PyMOL interfaces and a user manual! Scripts and data files for reproducing results reported in the DSSR-NAR paper. In MOVED: MD torsions. On May 03, 2016, 11:01:31 am. DSSR: Dissecting the Spatial Structure of RNA. March 28, 2015, 12:42:38 pm. October 31, 2013, 11:24:21 am. A question about base inclination.
MD simulations
http://forum.x3dna.org/md-simulations
Q&As related to 3DNA. An online community for DNA/RNA structural bioinformatics 3DNA. DSSR v1.6.1-2016aug22: an integrated software tool for Dissecting the Spatial Structure of RNA, with web/Jmol/PyMOL interfaces and a user manual! Analysis of Amber .mdcrd File. February 19, 2016, 01:16:22 pm. Generate DNA pdb file for Gromacs. January 21, 2016, 10:07:55 pm. X3dna ensemble extract output naming. December 05, 2015, 05:39:39 pm. How to Analysis the Conformation Parameters of Unnatural base in MD. April 01,...
base overlap
http://forum.x3dna.org/md-simulations/base-overlap/msg1924
Q&As related to 3DNA. An online community for DNA/RNA structural bioinformatics 3DNA. DSSR v1.6.1-2016aug22: an integrated software tool for Dissecting the Spatial Structure of RNA, with web/Jmol/PyMOL interfaces and a user manual! Topic: base overlap (Read 588 times). July 25, 2015, 03:55:43 am. Is there any way i could extract the stacked base overlap area as a function of time? Could i extract overlap area in analysis o/p. 171; Reply #1 on:. July 25, 2015, 09:34:41 am. Will the Ruby script.
Feature requests
http://forum.x3dna.org/feature-requests
Q&As related to 3DNA. An online community for DNA/RNA structural bioinformatics 3DNA. DSSR v1.6.1-2016aug22: an integrated software tool for Dissecting the Spatial Structure of RNA, with web/Jmol/PyMOL interfaces and a user manual! Request for new features. February 24, 2012, 03:00:30 pm. Four stranded i-motif build and reconstruction. August 15, 2016, 02:02:32 pm. July 11, 2016, 02:50:44 pm. August 12, 2015, 06:28:53 pm. Op1 op2. request for an option to keep the pdb header. June 26, 2014, 09:52:04 pm.
op1_op2. request for an option to keep the pdb header
http://forum.x3dna.org/feature-requests/op1_op2-request-for-an-option-to-keep-the-pdb-header/msg1582
Q&As related to 3DNA. An online community for DNA/RNA structural bioinformatics 3DNA. DSSR v1.6.1-2016aug22: an integrated software tool for Dissecting the Spatial Structure of RNA, with web/Jmol/PyMOL interfaces and a user manual! Op1 op2. request for an option to keep the pdb header. Topic: op1 op2. request for an option to keep the pdb header (Read 1674 times). Op1 op2. request for an option to keep the pdb header. June 26, 2014, 01:25:24 pm. Had taken care of the wrong anionic oxygen attributions.
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3DNA Homepage -- Nucleic Acid Structures
3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. Middot; Weird PDB entries. Middot; Highlights of recent developments of 3DNA/DSSR. Middot; Paulings triplex model of nucleic acids is available in 3DNA. Middot; 3DNA fiber models. Middot; PyMOL wrapper to 3DNA fiber models. As the name 3DNA may imply), but also to complicated RNA. Has been designed from the ground up to make RNA. 3DNA is under active development. In particular, ...
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