Any published work which has made use of 3DNA should cite at least one of the following papers:

The current list of journal articles citing 3DNA can be found in Google scholar.

In this section, I will occasionally highlight papers that employ 3DNA in novel or significant ways. If you have a story to share, please let me know.

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DSSR in the visualization of DNA/RNA structures

By following DSSR citations, I recently came across the article Interactive Visualization of RNA and DNA Structures by Lindow et al. The paper introduced a DNA/RNA visualization tool that integrates 1D sequence, 2D secondary structure in linear and graph representations, and 3D backbone ribbons and base ladders, all in one package. Notably, the 3D visualization was tailored for DNA/RNA structures and achieved quite impressive results. 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.

Overall, DSSR is an analysis/annotation tool that is supposedly agnostic to visualization programs. It derives a huge number of structural features that are unlikely to be matched elsewhere. I collaborated with Bob Hanson so that Jmol can directly take advantage of what DSSR has to offer, not just for the visualization of (modified) nucleotides and some common base pairs, but also the interactive selection of loops, pseudoknots, coaxial stacks, and various motifs. In particular, the SQL-like selection syntax Bob developed is really flexible and extremely powerful. I collaborated with Thomas Holder so that PyMOL can gain DNA/RNA domain knowledge. The resultant dssr_block PyMOL plugin is quite useful for creating base/base-pair block images with many revealing features, especially for small to medium-sized DNA/RNA structures. It is obvious to me that PyMOL (or any other molecular visualization tool) would benefit greatly from SQL-like selections of DSSR-derived features of nucleic acid structures, just as Jmol does.

In the Lindow et al. paper, some of the references to DSSR are technical in nature. Here, I’d like to respond and clarify each of them. Since DSSR is being actively developed and supported, I always welcome any feedback on the 3DNA Forum. Following and responding to literature represents another way that I strive to make DSSR a better tool to serve the community.

Built on their experience from 3DNA, Lu et al. developed DSSR [27], a very powerful tool to analyze RNA structures that uses Jmol for the 3D visualization. Recently, Hanson and Lu described this integration [10], which is based on a JSON-interface that directly couples DSSR and the 3D visualization of Jmol. This is a great improvement, but still missing is the integration of 2D secondary structure visualizations and brushing & linking techniques to enable simple selection with and exploration of the 3D molecular structure. One contribution of this paper is to show how a full linking between 3D and 2D visualizations can be done and what benefits arise from such a tight coupling (see Sects. 8 and 9).

This is a valid point, and the authors did a good job. Actually, one of the reviewers of our DSSR-Jmol paper brought up this point, and we acknowledged the limitation. While passing DSSR-derived secondary structural features (in DBN or .ct format) to a 2D visualization tool is straightforward, the connection would not be as smooth as we’d like it to be.

For this purpose, other approaches rely on the unique naming and ordering of the atoms [27], for example, N1, C2, N3, C4, C5, C6 etc. We found that this information is not always reliable.

The naming of the purines and pyrimidines follows the IUPAC standard and is a prerequisite of DNA/RNA structures in the PDB. In my experience, I have never found a single case where such information is not reliable. See below for abasic sites in PDB id 3BWP, and 4SU (4-thiouridine) in PDB id 5AFI.

We compared these results with the latest version of DSSR [27]. Our approach is able to correctly detect all regular nucleotides and most of the modified and undefined nucleotides. In the following, we describe the minor differences.

It is not clear what was the “latest” version of DSSR that was actually used in the paper. Note that DSSR has version info as in v1.8.3-2018oct29. I deliberately put the release date along with the version number.

For dataset 4RGE, we detected 3 modified uracil nucleotides that were not labeled as modified by DSSR. These nucleotides have a DNA backbone instead of an RNA one.

DSSR takes A, C, G, T, U as standard nucleotides, even if T is in RNA or U is in DNA. So this result is expected.

Dataset 3BWP contains 7 nucleotides that only consist of the backbone part without bases. While our approach marks these as undefined, in DSSR they are not detected at all.

The 7 nucleotides on 3BWP are abasic sites, i.e., without base atoms (N1, C2, N3, C4, C5, C6 etc), so they do not possess base reference frames. From early on, DSSR had the --abasic option for such cases. As of v1.7.3-2017dec26, DSSR directly incorporated abasic sites into the analysis. So thereafter they are detected by DSSR, by default.

Furthermore, in 5AFI we mark 3 nucleotides as undefined, while these are detected as a modified uracil by DSSR. This is due to the base containing sulfur instead of oxygen, so they possibly are sulfur analogs of uracil.

Presumably, the authors are referring to 4SU, 4-thiouridine, clearly a modified nucleotide occurring in 137 PDB entries (as of 2018oct28). DSSR detects three cases in 5AFI, as shown here: 4SU-u 3 v.4SU8,w.4SU8,y.4SU8

We also compared the results of our base pair detection (Suppl. Tab. 1). We determined all Watson-Crick, Hoogsteen, and Wobble pairs, and the reverse versions of the first two. For most of the datasets, our method returned the same results as DSSR. In particular, both approaches never created contradicting results, which means all common base pairs had identical pair type. In general, our geometrical approach generates slightly more base pairs compared to DSSR. However, when investigating both, the base pairs determined by DSSR but not by our approach and vice versa, we found that most of these pairs are border-line cases, where the decision was made depending on the threshold of the geometrical heuristic. Only in a few cases, the differences were not clear for both approaches, see Suppl. Fig. 3.

In Suppl. Fig. 3,

… However, the hydrogen bonds for classical G-U Wobble pairs seem to be quite unrealistic for the bottom left pair. Either this is a limitation of DSSR or it is some kind of specific Wobble pair with other hydrogen bonds than the depicted ones that our approach does not detect.

I echo the point that border-line cases could cause discrepancies between different methods. However, things can get easily clarified in concrete examples. Unfortunately, the authors did not specify the cases used in their Suppl. Fig. 3. I finally figured out the DSSR-assigned G-U Wobble pair in PDB id 1S72, U2586—G2592. As shown in the figure below, DSSR detects two H-bonds (dashed pink lines), "N3(imino)*N2(amino)[3.05],O4(carbonyl)-N1(imino)[2.77]". Note that one of the H-bonds is between two donors, N3(U) and N2(G), thus the * symbol. The H-bonds are by no means as those in “classical G-U Wobble pairs”. Yet, the pair is clearly Wobble-like, and that’s why it was assigned “Wobble”. To avoid such confusions, I’ve revised DSSR to tighten the criteria of G-U Wobble pair. As of v1.8.3-2018oct29, this pair is called "~Wobble".

DSSR-assigned ~Wobble pair]

Nevertheless, our evaluation (Sect. 8.1) shows that with the proposed approaches in terms of quality we get very similar results to the ones obtained by tools like DSSR. In terms of speed, DSSR needs much longer run times. For example, for 4U4O, DSSR needed ~15 min for the secondary and tertiary structure analysis [27], while our algorithm only needs ~0.2 s (see Tab. 1).

As noted above, DSSR provides far more structural features than just the identifications of nucleotides and several common base pairs. Even for the identified base pairs, DSSR provides many more annotations and structural parameters than just the named pairs picked by the authors. Not surprisingly, DSSR is slower than the dedicated method for a specific purpose.

As of DSSR v1.8.3-2018oct29, I’ve added the --pair-only option that just outputs a complete listing of base-pairing information and then stops. Some sample runs are as below:

x3dna-dssr -i=1ehz.pdb --pair-only
x3dna-dssr -i=1ehz.pdb --pair-only --more
x3dna-dssr -i=1ehz.pdb --pair-only --json
x3dna-dssr -i=1ehz.pdb --pair-only --json | jq '.pairs[] | select(.name=="WC")'
x3dna-dssr -i=1ehz.pdb --pair-only --more --json | jq .
x3dna-dssr -i=4u4o.cif --pair-only -o=4u4o-pairs.txt

Compared to the default settings, DSSR runs ~10 times faster when the --pair-only option is set; 36s vs 5m48s for 4U4O on my MacBook Pro 2017 (2.9 GHz Intel Core i7). Note the timing here is a complete run of the DSSR program (as shown above), from reading the mmCIF file to writing out all the derived features. In my hand, simply reading and parsing the 85MB 4U4O.cif would take ~5s. As a reference, just loading 4U4O.cif into PyMOL takes >6s. I’m thus more than surprised (and remain to be convinced) by the claim that their new algorithm “only needs” ~0.2s “for the secondary and tertiary structure analysis” of 4U4O.

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DSSR-enabled cartoon block images for G-quadruplex

Via Google Scholar, I noticed the recent publication in Nucleic Acids Research by Meier et al. titled Structure and hydrodynamics of a DNA G-quadruplex with a cytosine bulge. Reading through the article, I am pleased to see the section “Nucleic acid geometry and visualization” under MATERIALS AND METHODS:

We used the program DSSR (53) of the 3DNA suite (54) to analyse the nucleic acid backbone and the base pair geometry from the 3D structures. We reported the ‘simple’ base-pair parameters for buckle, propeller twist and stagger which are more intuitive for non-canonical base-pairs than the classic base-pair parameters as explained in the program manual and the 3DNA website (http://home.x3dna.org/highlights/details-on-the-simple-base-pair-parameters, http://home.x3dna.org/articles/simple-parameters-for-non-Watson-Crick-base-pairs). We wrote an R (55) script that automatically creates a backbone angle plot from the output of the DSSR program. The script can be downloaded from the 3DNA forum at http://home.x3dna.org. The nucleic acid was visualized in PyMOL and the dssr block plugin (The PyMOL Molecular Graphics Sys- tem, Version 2.0, Schro ̈dinger, LLC, https://pymol.org/). …

This is the first time (I’m aware of) that the ‘simple’ base-pair parameters introduced in 3DNA v2.3 is cited in a peer-reviewed journal article. I’m also glad to know that the blog posts on the 3DNA homepage are read, and even referenced in a publication — which surely will prompt me to write more. This is also the first time that the dssr_block PyMOL plugin is cited. I must say that Figures 1, 5, and 6 from the paper look gorgeous. Among other things, the G-tetrads and the surrounding base identity are immediately obvious using the simple color code: A, red; T, blue, C, yellow, and G, green. See Fig. 1 below.

DSSR-enabled block images [Fig. 1 of Meier18-nar-gky307]

In the section on “DATA AVAILABILITY”, the authors further noted:

Our R (55) script that automatically creates backbone angle plots from the output of the DSSR program can be downloaded from the 3DNA forum at http://home.x3dna.org.

I communicated with Markus Meier (the lead author) on the 3DNA Forum, on the thread DSSR: Analyzing NMR structures – overwritten output files. Checking the thread right now, I found that the R script (backbone_torsions_plot-1.0.tar.bz2) has been downloaded 263 times. I appreciate Markus’s effort in contributing the R script with a working example to the DSSR user community. It has always been my hope that more DSSR users would share their scripts and examples via the 3DNA Forum.

As a side note, I met Markus in Los Angles at the 60th Annual Meeting. It was a nice experience chatting with him, and had a lunch together. We’ve kept in touch following the meeting.

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SNAP is cited in the DNAproDB paper

I recently came across an article titled DNAproDB: an interactive tool for structural analysis of DNA-protein complexes by Sagendorf et al. in Nucleic Acids Research (NAR). Notably, the DNAproDB tool allows users to search the underlying database by combining features of the DNA, protein, or DNA-protein interactions at the interface. Compared to the well-established NUCPLOT tool which generates only ‘static’ schematic diagrams of protein-nucleic acid interactions, DNAproDB is interactive and more user friendly, with many new features.

It was a pleasant surprise to notice that SNAP was cited in the DNAproDB NAR paper, as follows:

Nucleotide-residue interaction geometry (stacking, pseudo-pairing or other) is determined using SNAP, a new component of the 3DNA program suite (35). SNAP also serves as a fall-back for calculating hydrogen bonds if HBPLUS cannot process the file.

I am glad that SNAP has also been used for identifying H-bonds where HBPLUS fails. The H-bonding detection algorithm, initially implemented in 3DNA (v2.3 and before) and refined in DSSR/SNAP, was originally intended to make the 3DNA software fully independent of third-party tools. I did not expect this feature could one day compete with dedicated H-bond finding tools, such as HBPLUS.

By the way, 3DNA is also cited in the DNAproDB NAR paper, as below:

DNA base pairing, shape parameters and conformation are derived from the 3DNA program suite (29) with a 10.0 Å cut-off for helix breaking.

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DSSR in the structural analysis of an E.coli initiator tRNAfMet A1-U72 variant

While browsing the latest issue (May 2017) of the RNA journal, I came across the paper titled The structure of an E. coli tRNAfMet A1–U72 variant shows an unusual conformation of the A1–U72 base pair by Monestier et al.. Reading through the text, I am pleasantly surprised by the two references to DSSR as shown below:

An analysis using DSSR (Lu et al. 2015) identifies all the secondary structure elements characteristic of the classical cloverleaf secondary structure as well as usual tertiary interactions that stabilize the L-shaped tertiary fold of the molecule.

As a consequence, the opening parameter (Lu et al. 2015) of the A1–U72 base pair becomes unusually high (153.42°). The NH2 group of A1 points toward the minor groove of the acceptor helix. An interaction between the N1 of A1 and the O2 of U72 (d = 3.0 Å) is observed which requires protonation of the N1 atom of A1.

The PDB id for the deposited structure is 5l4o. Running DSSR on this structure is straightforward: x3dna-dssr -i=5l4o.pdb --more. As with the classic yeast phenylalanine tRNA (PDB id: 1ehz), DSSR identifies two helices, three hairpin loops, one [2,1,5,0] four-way junction loop, among other features.

With regard to the unusual A1-U72 pair highlighted in the title of the paper, DSSR provides the following information. Note the * in the unconventional N1*O2 H-bond.

   1 A.A1           A.U72          A+U --          n/a       tWW  tW+W
       [-14.4(...) ~C3'-endo lambda=32.9] [-172.4(anti) ~C3'-endo lambda=65.0]
       d(C1'-C1')=10.80 d(N1-N9)=9.19 d(C6-C8)=10.68 tor(C1'-N1-N9-C1')=173.6
       H-bonds[1]: "N1*O2(carbonyl)[2.99]"
       interBase-angle=6  Simple-bpParams: Shear=3.53 Stretch=1.71 Buckle=2.0 Propeller=-6.0
       bp-pars: [-0.32   3.91    0.01    6.32    -0.26   153.56]

This citation is yet another example of DSSR’s adoption by experimental biologists. I can only expect to see more such type of DSSR usages in the coming years.

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DSSR is used in the URS DataBase

Recently, I came across the article URS DataBase: universe of RNA structures and their motifs by Baulin et al. in Database, an online journal of biological databases and curation. I am glad to see that DSSR is used in the URSDB, as quoted below.

In the “Input data” subsection of “Materials and methods”:

RNA-containing structures were extracted from the PDB in mmCIF format; each file was divided into models. The base pairs (both canonical and non-canonical) and dinucleotide steps were annotated using the DSSR program from 3DNA toolkit (26). We also exploited detailed information provided by DSSR on given elements such as geometric parameters, types according to different classifications and various details on base conformations.

Moreover, under “Future development”, the authors said:

We plan to perform a comparative analysis of programs that annotate base pairs in RNA-containing PDB files. We will consider the four most popular programs, FR3D (35), MC-Annotate (36), RNAView (37) and DSSR (26). According to the analysis the annotation of the base pairs will be refined. In addition, we plan to include in the database annotations of base-phosphate, base-ribose and base stacking contacts and to implement search of such data.

It is gratifying to see DSSR listed as one of “the four most popular programs” for annotating RNA base pairs. It’d also be interesting to see how DSSR compares with FR3D, MC-Annotate, and RNAView from the user’s perspective.

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DSSR in the validation of NMR RNA structures

With great interest, I read the article titled Improving NMR Structures of RNA by Bermejo et al. As is well-known, solution NMR structures of RNA normally exhibit more steric clashes and conformational ambiguities than their crystal X-ray counterparts. The paper introduces an improved force field, RNA-ff1, for structure elucidation with Xplor-NIH. By adopting realistic atom radii and a new statistical torsional potential, the RNA-ff1 force field significantly enhances covalent geometry and MolProbity validation scores (in steric contacts and backbone conformation) in the seven tested NMR datasets.

I am glad to see that DSSR is mentioned in the Section titled Analysis of Known Structural Motifs:

… The program DSSR (Lu et al., 2015) (part of the 3DNA software suite [Lu and Olson, 2003, 2008]) was used to evaluate the stacking configuration of successive base pairs (i.e., ‘‘steps’’) within the helical stems of the systems in the present calculations. The most interesting trends are observed for the base-pair step parameters slide (Figure 4K) and rise (Figure 4L), which respectively measure an in-plane dislocation and the vertical displacement of a step relative to a local mid-step reference frame (Lu and Olson, 2003; for analysis of all step parameters, see Figure S1). Relative to A-form parameters in high-resolution X-ray structures (Olson et al., 2001) (Figures 4K and 4L, dashed lines), the average slide of all but one of the original NMR models (PDB: 1O15) is small in absolute value (Figure 4K). … Moreover, four out of the seven original PDB models display an average rise considerably larger than the expected 3.32 Å (the van der Waals separation distance between bases, not to be confused with the helical rise, measured relative to the helical axis, expected to be 2.83 Å for A-form [Olson et al., 2001]).

As an example, the single stem of PDB: 2KOC’s representative structure, assumed to be an A-form helix (Nozinovic et al., 2010), displays a particularly large separation between base pairs C3–G12 and A4–U11 (rise: 4.33 Å) that is visually evident when compared with that of the RNA-ff1 representative model (rise: 3.33 Å ) (Figure 6A). Indeed, this base-pair step defies conformational classification by DSSR in the PDB: 2KOC structure, while it is assigned as A-form (along with the rest of the stem) in the RNA-ff1 structure.

Through the text, the term “stem” or “helical stem” is used consistently, in line with the nomenclatures adopted by DSSR. It is worth noting that DSSR also derives a complete set of backbone conformational parameters, including the assignment of sugar-phosphate backbone suites. The backbone parameters constitutes only a small portion of what DSSR has to offer, and they are written to the auxiliary file dssr-torsions.txt by default.

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First mention of SNAP in a peer-reviewed journal article

The other day, I came across an article titled Different duplex/quadruplex junctions determine the properties of anti-thrombin aptamers with mixed folding by Krauss et al. published in Nucleic Acids Research (NAR). This NAR article draw my attention via Google Scholar alert because of its citation to the 2008 3DNA Nature Protocols paper, as shown below (in the Structural analysis section):

3DNA-dssr (41) was used to calculate local and overall geometric parameters of the aptamer. Superpose program from CCP4 package (42) was used to calculate root mean square deviations. Features of the thrombin–RE31 interface were calculated using Cocomaps server (43), whereas contacts between the two molecules, as well as packing interactions between the aptamer and symmetry related thrombin molecules, were found by using 3DNA-snap (41) and Pisa (44) programs. All the results were veri ed by visual inspec- tion of the structure with WinCoot (39).

Moveover, Table 2 lists Stacking interactions as calculated by 3DNA-DSSR (41) among residues belonging to the duplex, the junction and the quadruplex of RE31, with a note on the definition of base-stacking interactions:

Base-stacking is quantified as the area of the overlapped polygon de ned by the two bases of the interacting nucleotides, where the base atoms are projected onto the mean base plane.

To the best of my knowledge, this is the first time SNAP is mentioned in a peer-reviewed journal article. This paper also made good use of DSSR for the analysis of a complicated DNA structure (like RNA), with three non-canonical base pairs at the duplex/quadruplex junction (Figure 3) and extensive stacking interactions (Figure 4).

The duplex/quadruplex junction in RE31 aptamer.
Figure 3. The duplex/quadruplex junction in RE31 aptamer.

Ribbon representation of RE31 highlighting the continuous stacking of bases from the duplex to the quadruplex region.
Figure 4. Ribbon representation of RE31 highlighting the continuous stacking of bases from the duplex to the quadruplex region.

As this paper and those by Paul Paukstelis illustrate, DNA can adopt far more complicated 3D structures enabled by non-canonical base pairing schemes than the simple Watson-Crick paired double helices. 3DNA (including DSSR and SNAP) is well suited for the analysis of such extraordinary structures. On a different perspective, following 3DNA citations has become an effective way for me to keep in pace with relevant literature.

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First citation to the DSSR NAR paper in JMB

Recently, I noticed via Google Scholar the first citation to the paper DSSR, an integrated software tool for dissecting the spatial structure of RNA, recently published in Nucleic Acids Research (NAR). The citation is from Srinivas Somarowthu, in a review article titled Progress and current challenges in modeling large RNAs in the Journal of Molecular Biology. The JMB review article is concise, and overall a nice reading.

Specifically, in the section “Model Evaluation and Refinement”, DSSR is listed along with RNAView and MC-Annotate for the characterization of the secondary from 3D atomic coordinates, as below:

After building a model, it is essential to evaluate the quality, find any errors and refine the accordingly. First, it is important to make sure that all the base-pairs and the overall secondary structure is maintained correctly in the model. Tools such as RNAview [82], MC-Annotate [83], and DSSR [84] can calculate the secondary structure from a given 3D structure and thereby allow identification of problematic base-pairs. Recently, Antczak et al [85], developed a web server, RNApdbee, which integrates RNAview, MC-Annotate and DSSR, and extracts not only secondary structures but also kissing-loops and pseudoknots from a target tertiary model. Problematic base pairs can be fixed or rebuilt using interactive tools such as S2S/ASSEMBLE [45].

I am glad to see the first citation to the 2015 DSSR paper per se shortly after its publication in NAR. Looking forward, I can only expect more DSSR citations in diverse fields related to RNA structures.

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Citation statistics to 3DNA publications

On October 29, 2015, I performed a survey of citations to the following three 3DNA papers, using the Web of Science. The total number of citations are: NAR03 (787) + NP08 (184) + NAR09 (78) = 1049, spanning a diverse set of 191 journals in biology, chemistry, and material sciences. On the same date, Google Scholar reported 1360 citations for the same three papers.

  1. [NAR03] Lu, Xiang‐Jun, and Wilma K. Olson. “3DNA: a software package for the analysis, rebuilding and visualization of three‐dimensional nucleic acid structures.” Nucleic acids research 31.17 (2003): 5108-5121.
  2. [NP08] Lu, Xiang-Jun, and Wilma K. Olson. “3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures.” Nature protocols 3.7 (2008): 1213-1227.
  3. [NAR09] Zheng, Guohui, Xiang-Jun Lu, and Wilma K. Olson. “Web 3DNA—a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures.” Nucleic acids research 37.suppl 2 (2009): W240-W246.

Among the 1049 citations in 191 journals, 694 citations (66%) are from the following 24 journals (~13%). The remaining 355 citations are from 167 other journals, including Cell (5 times), Science (2), Nature (3) and six additional Nature Publishing Group sub-journals (17).

1 Nucleic Acids Res (167)
2 J Phys Chem B (64)
3 Biochemistry (45)
4 J Am Chem Soc (45)
5 J Mol Biol (41)
6 Phys Chem Chem Phys (28)
7 Biophys J (25)
8 J Biol Chem (23)
9 PLoS One (23)
10 Acta Crystallogr D Biol Crystallogr (22)
11 J Chem Theory Comput (22)
12 Proc Natl Acad Sci U S A (22)
13 Bioinformatics (18)
14 Biopolymers (18)
15 J Biomol Struct Dyn (18)
16 J Chem Phys (18)
17 J Phys Chem A (16)
18 Structure (13)
19 RNA (12)
20 Biochem Biophys Res Commun (11)
21 Chem Res Toxicol (11)
22 J Comput Chem (11)
23 J Mol Model (11)
24 Nat Struct Mol Biol (10)

It is worth noting that while the Web of Science citation report is comprehensive, it is certainly not complete. In particular, citations in the online methods section seem not to be covered. For example, two 3DNA citations (on the DSSR program) in “Materials and Methods” (the Supplementary Materials) of two Science articles by the Ramakrishnan lab are missing from the list. Specifically, the Science papers employed DSSR for the characterization of RNA secondary structural features in crystal structures of the large ribosomal subunit and the whole ribosome of human mitochondria.

For those why are interested in knowing the details, click the link for the full reports of 3DNA citations. In the file, the citations are sorted in two ways: by citation numbers per journal, and by journal names.

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Thank you for printing this article from http://home.x3dna.org/. Please do not forget to visit back for more 3DNA-related information. — Xiang-Jun Lu