X3dna program

The software remains free for academic users, with the basic user manual. The professional user manual over pages, including 7 appendices is available for paid academic users or commercial users only. Licensing revenue helps ensure the long-term sustainability of the DSSR project. Check the web interface. The time range is from to June 30 , for a total of five-and-half years.

The 1, citations span scientific journals, covering a broad range of research fields such as biology, medicine, chemistry, physics, materials etc. Each of following six papers has been cited over 50 times, as detailed below. The top 21 journals that cite 3DNA papers 10 times or more are listed below.

The numbers were 3, on October 15, , 2, on on February 3, , and 1, on February 27, respectively. For year , the monthly registrations are 36 January , 35 February , 54 March , 84 April , 69 May.

As of June 26, the number is 56, which will more than likely pass 60 by the end of this month. The Covid pandemic does not seem to having a negative effect on the registrations.

The over 5, registrations are from users all over the world. The 3DNA Forum remains spam free, and all questions are promptly answered. It is functioning well; certainly better than I originally imagined. Overall, the Forum serves as a virtual platform for me to interact effectively with the ever-increasing user community. Please do not forget to visit back for more 3DNA-related information. Search What's new? Acta Cryst F Upon binding TO1-biotin, the iMango- III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers over fold.

Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition. Nucleic Acids Res. Adenosine deaminase enzymes convert adenosine to inosine in duplex RNA , a modification that strongly affects RNA structure and function in multiple ways. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.

Nat Commun Mol Cell Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators. Nat Struct Mol Biol T-box riboregulators are a class of cis-regulatory RNA s that govern the bacterial response to amino acid starvation by binding, decoding, and reading the aminoacylation status of specific transfer RNA s. Nucleic Acids Res A large number of hereditary neurodegenerative human diseases are associated with abnormal expansion of repeated sequences.

RNA containing CAG repeats can be recognized by synthetic cyclic mismatch-binding ligands such as the structure shown. Cell Chem Biol The fluorescent compound Thioflavin T, widely used for the detection of amyloids, is bound at the dimer interface of the homodimeric G-quadruplex-containing RNA Corn aptamer.

Nme1Cas9, a compact nuclease for in vivo genome editing. Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths. Nucleic Acids Res — This process has helped us to refine and improve the software and has prompted us to add new functionality. Today, 3DNA has become a prominent structural bioinformatics tool, and is widely used in the scientific community.

Xiang-Jun Lu during to while working as a post-doctoral research associate in Dr. Thereafter, Dr. Lu — in collaboration with Dr. Olson — had continued to maintain and support 3DNA in his spare time as a sideline project. Lu is now dedicated to pushing 3DNA to the next level to better serve the ever-changing needs of an ever-growing user community. We are working on a new release currently in beta test of 3DNA v2. Comment [2].

Unless specified explicitly otherwise, all posts at x3dna. The favicon and logo of the homepage and the forum were designed by Jessalyn Lu. Please do not forget to visit back for more 3DNA-related information. Search What's new? Added the --g4-onz option for ONZ classifications of G-tetrads in intramolecular G-quadruplexes , plus minor code refinements. Fixed a bug in the identification of junction loops in special cases as in PDB entry: 4wsm — thanks to lijun for reporting.

Fixed a bug in reported base-stacking areas in special cases. Added a list of modified nucleotides such as 5CM to the main output as in DSSR ; Fixed a bug in rare cases, plus miscellaneous code refinements. Checked the compatibility of the --symm option with an NMR -ensemble-like input file where only the first model is handled; enhanced features on the analysis and output of G-quadruplexes; revised identification of duplex-G4 junctions e.

Refined the code for command-line options; Added --block-opt or --block-option as an alternative for --block-file. Revised the algorithm for the alignment of G-tetrads along a G-helix.

Now the left-handed G-quadruplex 6fq2 has a Twist angle of Revised the --analyze-cehs option so that for non-WC structures it gives consistent results with the cehs program in 3DNA v2. Revised the cehs program for characterizing non-WC pairs. Added the --analyze option to output a list of key structural parameters as those from the 3DNA v2.

This option can also be specified as dna-v2 , and it contains variations to fit other potential needs. Relaxed criteria for reverse Hoogsteen rHoogsteen pairs; revised the algorithm for base identification in special cases.

Refined code and fixed a couple of bugs in rare occasions. Refined the algorithm for H-bonds, plus documentation improvements and code refactoring. SNAP is mature and robust enough for version 1. For example, for str 2, the BR atom is now in the modified nucleotide 5BU for 5-bromouridine.

As a result, helical parameters Twist, Rise etc. Indeed, over the years following citations to DSSR has become an effective way for me to become informed of directly relevant references. Reading these citing articles motivates me to further improve DSSR. I recently come across the article FMN riboswitch aptamer symmetry facilitates conformational switching through mutually exclusive coaxial stacking configurations by Wilt et al. The LW scheme is based on the three edges of each base with potential for H-bonding interactions Watson-Crick, Hoogsteen, and Sugar , and the two orientations cis or trans of the interacting bases with respect to the glycosidic bonds.

This geometry-based approach captures salient features of pairing interactions and strikes a balance between simplicity and expressiveness. The LW scheme is more widely applicable than the Saenger classification, and more intuitive to biologists.

There are numerous pairs in RNA with only one H-bond or with bifurcated H-bonds, at boundary locations where the LW classification does not strictly apply. Lemieux and Major were the first to extend the LW classification. Finally, the RNA 3D Hub website , hosted by the Leontis-Zirbel team, lists pairing interactions that do not fall into the 12 geometric types. As shown in the figure above, DSSR adopts a base-centric terminology for the three edges. The abstract is as below:.

Highly structured RNA molecules usually interact with each other, and associate with various RNA -binding proteins, to regulate critical biological processes. However, RNA structures and interactions in intact cells remain largely unknown. This technique not only recapitulates known RNA secondary structures and tertiary interactions, but also facilitates the generation of three-dimensional 3D interaction maps of RNA in human cells.

Using these maps, we identify noncoding RNA targets globally, and discern RNA topological domains and trans-interacting hubs. We reveal that the functional connectivity of enhancers and promoters can be assigned using their pairwise-interacting RNA s. Our study demonstrates the power and applicability of RIC -seq in discovering the 3D structures, interactions and regulatory roles of RNA.

The Methods part contains the following section, where DSSR is cited along with several other software tools:. Structural analysis of 28S rRNA. A Knight—Ruiz normalization al- gorithm, widely used in the normalization of Hi-C contact matrices 51 , was applied to eliminate sequencing bias along rRNA.

One may wonder why DSSR is used here. In addition to asking the authors, interested viewers could simply test for themselves: try the different tools on PDB entry 4V6X and see what happens. I will shortly write another post on this topic when this paper is officially published online. Sophisticated analysis and simplified visualization are crucial for understanding complicated structures of biomacromolecules. The program creates schematic block representations in diverse styles that can be seamlessly integrated into PyMOL and complement its other popular visualization options.

In addition to portraying individual base blocks, DSSR can draw Watson-Crick pairs as long blocks and highlight the minor-groove edges. Notably, DSSR can dramatically simplify the depiction of G-quadruplexes by automatically detecting G-tetrads and treating them as large square blocks. The DSSR -enabled innovative schematics with PyMOL are aesthetically pleasing and highly informative: the base identity, pairing geometry, stacking interactions, double-helical stems, and G-quadruplexes are immediately obvious.

These features can be accessed via four interfaces: the command-line interface, the DSSR plugin for PyMOL, the web application, and the web application programming interface. The supplemental PDF serves as a practical guide, with complete and reproducible examples. This 1.

Protein conservation mapping to the structure was done using the Consurf server Ashkenazy et al. Structure validation statistics were generated with MolProbity Chen et al. In the main text, the authors cited DSSR for the detection of a base multiplet.

In the figure above, each of the two adenines is interacting with a G—C pair in the minor-groove edge m of the pair: A30 left is using its Watson-Crick edge W , whilst A23 right is employing its major-groove edge M. Thus they do not belong to the canonical A-minor motifs types I or II where the minor-groove edge of A interacts with the minor-groove edge of a WC pair. A nice feature of the 2D graph representation is the handling of multiple chains.

Reading through the main text and the supplementary material, I was surprised to see the so many locations where DSSR was mentioned, especially the following:. Our approach detects all standard and many modified nucleotides as well as the most common base pairs. Further special cases could be easily added. Yet, the system we developed should not be seen as a replacement for well established tools like DSSR.

Rather, it shows what can be achieved with modern techniques in terms of both computation and rendering. It derives a huge number of structural features that are unlikely to be matched elsewhere.