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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://www.x3dna.org/
Homepage of the 3DNA suite of software programs for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures
http://www.x3dna.org/
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Xiang-Jun Lu
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Xiang-Jun Lu
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3DNA Homepage -- Nucleic Acid Structures | x3dna.org Reviews
https://x3dna.org
Homepage of the 3DNA suite of software programs for the analysis, rebuilding and visualization of 3-dimensional nucleic acid structures
3DNA Forum - Index
Q&As related to 3DNA. An online community for DNA/RNA structural bioinformatics 3DNA. Did you miss your activation email. DSSR-Jmol featured in the cover image. Of NAR'17 web-server issue; DSSR v1.7.6-2018mar22 is out, featuring an analysis/annotation of G-quadruplexes, and the. Messages from the site administrator on 3DNA. In Re: Highlights of recent. On February 02, 2018, 02:13:42 am. Request for new features. In Re: Rebuild DNA structur. On November 06, 2017, 09:06:39 am. In Re: Trouble running 3DNA.
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, ...
DSSR-Jmol Web Interface
DSSR-Enhanced Visualization of Nucleic Acid Structures in Jmol. Robert M. Hanson and Xiang-Jun Lu. To gain full access to Jmol scripting, and see the. The commands issued above are echoed in the text box. Other Jmol scripts can also be input there (see examples). Right-click (or Ctrl-click on Mac. In the image window to see the contextual menu. SELECT @{ M.dssr.nts.select("WHERE is modified")}. For modified nucleotides, or. SELECT @{ M.dssr.pairs.select("WHERE name!
Web Interface to DSSR
Web interface to DSSR. Welcome to the web interface to DSSR. An integrated software tool for Dissecting the Spatial Structure of RNA. This simple website aims to showcase key features of the program by providing its. Output file. To take full advantage of DSSR. The program and run it locally. Note that the uploaded file or filled-in coordinates must be in. Format, and be less than five megabytes (5MB) in size. Please specify a PDB id, upload a file, or fill in coordinates.
Web Interface to SNAP
Web interface to SNAP. Welcome to the web interface to SNAP. An integrated software tool for the characterization of three-dimensional Structures of Nucleic Acid-Protein complexes. This simple website aims to showcase key features of the program by providing its. Output file. To take full advantage of SNAP. The program and run it locally. Note that the uploaded file or filled-in coordinates must be in. Format, and be less than two megabytes (2mb) in size. By Dr Xiang-Jun Lu xiangjun@x3dna.org.
Web Interface to DSSR
Web interface to DSSR. Welcome to the web interface to DSSR. An integrated software tool for Dissecting the Spatial Structure of RNA. This simple website aims to showcase key features of the program by providing its. Output file. To take full advantage of DSSR. The program and run it locally. Note that the uploaded file or filled-in coordinates must be in. Format, and be less than two megabytes (2mb) in size. Please upload a file or fill in coordinates, and set options.
x3dna.org
3DNA Homepage -- Nucleic Acid Structures
http://x3dna.org/articles/conformation-of-the-sugar-ring-in-nucleic-acid-structures
3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. 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. Analyzing DNA/RNA structures with Curves and 3DNA. Parsing DSSR json output. Updates on x3dna.org. And phase angle (.
3DNA Homepage -- Nucleic Acid Structures
http://x3dna.org/articles/the-dssr-prefix-and-cleanup-options
3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. 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. Analyzing DNA/RNA structures with Curves and 3DNA. Parsing DSSR json output. Updates on x3dna.org. Code, I do feel that ...
3DNA Homepage -- Nucleic Acid Structures
http://x3dna.org/articles/dssr-derived-dbn-for-an-input-entry-with-multiple-rna-molecules
3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. 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. Analyzing DNA/RNA structures with Curves and 3DNA. Parsing DSSR json output. Updates on x3dna.org. Chains (molecules)...
3DNA Homepage -- Nucleic Acid Structures
http://x3dna.org/articles/outside-links
3DNA: a suite of software programs for the analysis, rebuilding and visualization of 3-Dimensional Nucleic Acid structures. 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. Analyzing DNA/RNA structures with Curves and 3DNA. Parsing DSSR json output. Updates on x3dna.org. 8212; 3DNA-Driven DNA.
3DNA Homepage -- Nucleic Acid Structures
http://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. 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. Analyzing DNA/RNA structures with Curves and 3DNA. Parsing DSSR json output. Updates on x3dna.org. Global bending of DNA.
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SBGrid Consortium - Supported Applications
https://www.sbgrid.org/software
SBGrid In Your Lab. Structure Visualization and Analysis. Structure Visualization and Analysis. No programs selected How to use AppCiter? How to use AppCiter? AppCiter will help you create a bibliography of the programs you wish to cite. 1 Choose Your Programs. Button in the Name column to choose your programs. Proceed to Step 2 to view available citations. Select citations from a custom list. Proceed to Step 3 to download. Export citations or send them to your email. Continue to Step 2. The structure-so...
Xiang-Jun's Corner: Curves+ vs 3DNA
http://xiang-jun.blogspot.com/2009/08/curves-vs-3dna.html
Random thoughts, mostly on scientific issues. Sunday, August 16, 2009. While browsing Nucleic Acids Research. Recently, I noticed the paper titled " Conformational analysis of nucleic acids revisited: Curves. Anyone who has ever worked on nucleic acid structures (especially DNA) should be familiar with Curves. An analysis program that has been widely used over the past twenty years. Only in recent years has 3DNA become popular. On June 6, 2003. And emphasized again on June 09, 2003. We also see Curves un...
Xiang-Jun's Corner: Sugar pucker correlates with phosphorus-related distance
http://xiang-jun.blogspot.com/2011/06/sugar-pucker-correlates-with-phosphorus.html
Random thoughts, mostly on scientific issues. Sunday, June 19, 2011. Sugar pucker correlates with phosphorus-related distance. The sugar puckers in DNA/RNA structures are predominately in either C3'-endo or C2'-endo (see Figure below), corresponding to the A- or B-form conformation in a DNA duplex. Recently, I (re-)read a few articles related to the RNA backbone by Jane Richardson et al. RNA backbone is rotameric. RNA backbone: consensus all-angle conformers and modular string nomenclature. Out of curios...
Xiang-Jun's Corner: GpU dinucleotide platform, the smallest unit with key RNA structural features
http://xiang-jun.blogspot.com/2011/07/gpu-dinucleotide-platform-smallest-unit.html
Random thoughts, mostly on scientific issues. Thursday, July 14, 2011. GpU dinucleotide platform, the smallest unit with key RNA structural features. Compared to DNA, RNA has three salient structural features: it contains ribose sugar, uracil, and is normally single-standed. The O2'(G).O2P(U) H-bond stabilized GpU dinucleotide platform. May turn out to be the smallest unit with all those RNA hallmarks (see Figure below). Firstly, it must have the guanosine ribose to form the O2'(G).O2P(U) H-bond.
Xiang-Jun's Corner: July 10, 2011
http://xiang-jun.blogspot.com/2011_07_10_archive.html
Random thoughts, mostly on scientific issues. Thursday, July 14, 2011. GpU dinucleotide platform, the smallest unit with key RNA structural features. Compared to DNA, RNA has three salient structural features: it contains ribose sugar, uracil, and is normally single-standed. The O2'(G).O2P(U) H-bond stabilized GpU dinucleotide platform. May turn out to be the smallest unit with all those RNA hallmarks (see Figure below). Firstly, it must have the guanosine ribose to form the O2'(G).O2P(U) H-bond.
Xiang-Jun's Corner: July 24, 2011
http://xiang-jun.blogspot.com/2011_07_24_archive.html
Random thoughts, mostly on scientific issues. Friday, July 29, 2011. Tracking 3DNA citations: Google scholar vs. Web of Science. Over the years, I have been following citations to 3DNA on a regular basis. Using both Google Scholar. And Web of Science. From a personal perspective, following the citations has turned out to be an excellent way to keep myself informed of progress related to nucleic acid structures. Up to early this year, I had found 3DNA citations based on Google Scholar. And Web of Science.
Xiang-Jun's Corner: October 23, 2011
http://xiang-jun.blogspot.com/2011_10_23_archive.html
Random thoughts, mostly on scientific issues. Tuesday, October 25, 2011. Mutate bases, a new 3DNA tool for in silico base mutations of 3D nucleic acid structures. In response to repeated requests from 3DNA users over the years, I recently (well, a few months ago) released a new utility program, mutate bases. To the 3DNA suite of software package. As its name implies, mutate bases. Is a standalone ANSI C program, on a par with other major 3DNA programs (e.g., find pair. Is designed to solve the base mutat...
Xiang-Jun's Corner: March 04, 2012
http://xiang-jun.blogspot.com/2012_03_04_archive.html
Random thoughts, mostly on scientific issues. Friday, March 9, 2012. X3dnaorg - 3DNA's new home. It has been quite a while since my last blog post titled "3DNA base-mutation functionality for the study of pretein-DNA interactions" (dated Sunday, October 30, 2011). Over the past few months, I have been extremely busy laying the groundwork for 3DNA: both in software consolidation and hardware setup. Here are some background details about what happened:. 3DNA now has a dedicated domain name x3dna.org. Power...
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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; DSSR has been published, and its results are reproducible. Middot; Conformation of the sugar ring in nucleic acid structures. Middot; The DSSR - prefix and - cleanup options. Middot; Assignment of HETATM vs. ATOM records for modified nucleotides in PDB vs. PDBx/mmCIF format. Middot; The value of tiny and self-contained software in the big-data era. And have facilities for th...
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