Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. [Nucleic Acids Res 48: e74(https://doi.org/10.1093/nar/gkaa426)).

See the 2020 paper titled "DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL" in Nucleic Acids Research and the corresponding Supplemental PDF for details. Many thanks to Drs. Wilma Olson and Cathy Lawson for their help in the preparation of the illustrations.

Details on how to reproduce the cover images are available on the 3DNA Forum.


May 2025

May 2025

Complex of terminal uridylyltransferase 7 (TUT7) with pre-miRNA and Lin28A (PDB id: 8OPT; Yi G, Ye M, Carrique L, El-Sagheer A, Brown T, Norbury CJ, Zhang P, Gilbert RJ. 2024. Structural basis for activity switching in polymerases determining the fate of let-7 pre-miRNAs. Nat Struct Mol Biol 31: 1426–1438). The RNA-binding pluripotency factor LIN28A invades and melts the RNA and affects the mechanism of action of the TUT7 enzyme. The RNA backbone is depicted by a red ribbon, with bases and Watson-Crick base pairs represented as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; TUT7 is represented by a gold ribbon and LIN28A by a white ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).


April 2025

April 2025

Cryo-EM structure of the pre-B complex (PDB id: 8QP8; Zhang Z, Kumar V, Dybkov O, Will CL, Zhong J, Ludwig SE, Urlaub H, Kastner B, Stark H, Lührmann R. 2024. Structural insights into the cross-exon to cross-intron spliceosome switch. Nature 630: 1012–1019). The pre-B complex is thought to be critical in the regulation of splicing reactions. Its structure suggests how the cross-exon and cross-intron spliceosome assembly pathways converge. The U4, U5, and U6 snRNA backbones are depicted respectively by blue, green, and red ribbons, with bases and Watson-Crick base pairs shown as color-coded blocks: A/A-U in red, C/C-G in yellow, G/G-C in green, U/U-A in cyan; the proteins are represented by gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).


February 2025

February 2025

Structure of the Hendra henipavirus (HeV) nucleoprotein (N) protein-RNA double-ring assembly (PDB id: 8C4H; Passchier TC, White JB, Maskell DP, Byrne MJ, Ranson NA, Edwards TA, Barr JN. 2024. The cryoEM structure of the Hendra henipavirus nucleoprotein reveals insights into paramyxoviral nucleocapsid architectures. Sci Rep 14: 14099). The HeV N protein adopts a bi-lobed fold, where the N- and C-terminal globular domains are bisected by an RNA binding cleft. Neighboring N proteins assemble laterally and completely encapsidate the viral genomic and antigenomic RNAs. The two RNAs are depicted by green and red ribbons. The U bases of the poly(U) model are shown as cyan blocks. Proteins are represented as semitransparent gold ribbons. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).


January 2025

January 2025

Structure of the helicase and C-terminal domains of Dicer-related helicase-1 (DRH-1) bound to dsRNA (PDB id: 8T5S; Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL. 2024. Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. eLife 13: RP93979. Cryo-EM structures of Dicer-1 in complex with DRH-1, RNAi deficient-4 (RDE-4), and dsRNA provide mechanistic insights into how these three proteins cooperate in antiviral defense. The dsRNA backbone is depicted by green and red ribbons. The U-A pairs of the poly(A)·poly(U) model are shown as long rectangular cyan blocks, with minor-groove edges colored white. The ADP ligand is represented by a red block and the protein by a gold ribbon. Cover image provided by X3DNA-DSSR, an NIGMS National Resource for structural bioinformatics of nucleic acids (R24GM153869; skmatics.x3dna.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).


Moreover, the following 30 [12(2021) + 12(2022) + 6(2023)] cover images of the RNA Journal were generated by the NAKB (nakb.org).

Cover image provided by the Nucleic Acid Database (NDB)/Nucleic Acid Knowledgebase (NAKB; nakb.org). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

DSSR-PyMOL cartoon blocks generated by the NDB/NAKB

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It gives me great pleasure to announce that the 3DNA/DSSR project is now funded by the NIH R24GM153869 grant, titled "X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids". I am deeply grateful for the opportunity to continue working on a project that has basically defined who I am. It was a tough time during the funding gap over the past few years. Nevertheless, I have experienced and learned a lot, and witnessed miracles enabled by enthusiastic users.

Since late 2020 when I lost my R01 grant, DSSR has been licensed by the Columbia Technology Ventures (CTV). I appreciate the numerous users (including big pharma) who purchased a DSSR Pro License or a DSSR Basic paid License. Thanks to the NIH R24GM153869 grant, we are pleased to provide DSSR Basic free of charge to the academic community. Academic Users may submit a license request for DSSR Basic or DSSR Pro by clicking "Express Licensing" on the CTV landing page. Commercial users may inquire about pricing and licensing terms by emailing techtransfer@columbia.edu, copying xiangjun@x3dna.org.

DSSR v2.4.5-2024sep24 was released to synchronize with the new R24 funding, which will bring the project to an entirely new level. All existing users are encouraged to upgrade their installation to this release which contains miscellaneous bug fixes (e.g., chain id with > 4 chars) and numerous minor improvements.

Lots of exciting things will happen for the project. The first thing is to make DSSR freely accessible to the academic community. In the past couple of weeks, CTV have already issued quite a few DSSR Basic Academic licenses to users from all over the world. So the demand is high, and it will become stronger as more academic users become aware of DSSR. I'm closely monitoring the 3DNA Forum, and is always ready to answer users questions.

I am committed to making DSSR a brand that stands for quality and value. By virtue of its unmatched functionality, usability, and support, DSSR saves users a substantial amount of time and effort when compared to other options. My track record throughout the years has unambiguously demonstrated my dedication to this solid software product.


DSSR Basic contains all features described in the three DSSR-related papers, and includes the originally separate SNAP program (still unpublished) for analyzing DNA/RNA-protein complexes. The Pro version integrates the classic 3DNA functionality, plus advanced modeling routines, with email/Zoom/phone support.

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G-quadruplex -- notes on ASC-G4

Recently, I read carefully the two papers by Farag et al. on the ASC-G4 algorithm to calculate "advanced structural characteristics of G-quadruplexes" (2023), and the comprehensive analysis results of intramolecular G4 structures in the PDB (2024). By developing a convention to orient and number the four strands, ASC-G4 allows for unambiguous determination of the intramolecular G4 topology. It also has an in-depth discussion on assigning syn or anti glycosidic configuration of guanosines, and categorizes four different types of snapbacks.

I am glad to see that DSSR is cited in these two papers, as quoted below:

X3dna-DSSR (19) (http://x3dna.org) is a website that was created to calculate nucleic acid structural parameters, like the local base-pair parameters, local step base-pair parameters, torsion angles, etc, but not the special characteristics of G4. A subdomain dedicated to G4, DSSR-G4DB (Dissecting the Spatial Structure of RNA – G4 Data Base) (http://g4.x3dna.org) emanated from this website. It is a database that gathers and calculates some specific structural information about published G4s, like the topology, the rise, the helical twist, etc, but not the groove widths or the presence of snapbacks. -- Farag et al. (2023) 

Indeed, DSSR-G4DB dose not classify snapbacks. I was aware of such non-canonical G4s when I first developed the G4 module in DSSR around 2017-2018, and the V-shaped loops was derived to reflect the peculiarity of snapbacks.

DSSR classifies groove widths as medium, wide, or narrow, based on the glycosidic angles of neighboring guanosines in a G-tetrad, following the G4 literature. Using PDB entry 2lod as an example, the relevant part of the DSSR output is shown below. The groove widths of the three G-tetrads in the G4-stem have the same pattern of groove=--wn, standing for medium, medium, wide, and narrow, respectively. Note that the medium groove is represented by a dash instead of m because --wn stands out more clearly than mmwn (similar idea applies to glycosidic bond, e.g., sss-).

 1  glyco-bond=sss- sugar=---- groove=--wn Major-->WC N- nts=4 GGGG A.DG1,A.DG6,A.DG20,A.DG16
 2  glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG2,A.DG7,A.DG21,A.DG15
 3  glyco-bond=---s sugar=---- groove=--wn WC-->Major N+ nts=4 GGGG A.DG3,A.DG8,A.DG22,A.DG14

Since DSSR-G4DB is a database, the user cannot provide his own G4 structure, to obtain structural information. Hence the necessity of developing a website where the user uploads his G4 structure file to obtain all its important and specific structural characteristics (like the topology, the groove width, the tilt and twist angles, etc.). This can be very useful, not only for the analysis of published PDB structures but also for structures in refinement or obtained from MD simulations, to evaluate their quality. To our knowledge, there is no website dedicated to G4 to do such calculations in real-time. Therefore, we developed the algorithm ASC-G4 (advanced structural characteristics of G4) and deployed it as a user-friendly website at the following address: http://tiny.cc/ASC-G4. -- Farag et al. (2023)

Thanks to the NIH R24GM153869 grant support, the http://g4.x3dna.org website now allows users to upload their own atomic structures in PDB for mmCIF format for the identification, annotation, and visualization of G4s. See the example of uploading PDB coordinate file 2lod.pdb.

As background, I had long aspired to develop a dynamic website for on-demand G4 structural analysis but was unable to pursue this goal until recently. During the 4-year funding gap, I still managed to maintain the website g4.x3dna.org, which provides DSSR results for G4 structures in the PDB (a resource now known as the DSSR-G4DB database). To date, the only published work related to G4s is my 2020 paper on the integration of DSSR with PyMOL. Clearly, a dedicated method paper detailing the G4 module in DSSR and the g4.x3dna.org website has been long overdue.

As an initial step toward addressing this gap, I have recently revised the G4-related code in DSSR, fixed existing bugs, and added new features. The g4.x3dna.org website has undergone a complete overhaul, enabling users to upload their own structures for dynamic G4 analysis. Additionally, the DSSR-G4DB database is being actively updated on a weekly basis as new PDB entries are added.

Calculation of the twist and tilt angles. In G4, the helix twist is the rotation of a tetrad relative to its successive one. To measure the twist angle, the most spread method is that described by Lu and Olson (2003) (32) and Reshetnikov et al. (2010) (33). In this method, the angle is calculated from the dot product between two C1’–C1’ vectors from two successive tetrads, i and i + 1, the C1’ atoms of each vector belonging to two adjacent guanosines of a Hbp. The issue with this method is that it does not allow access to the sign of the angle, which defines the direction of the G4 helix, viz. right-handed or left-handed. -- Farag et al. (2023)

There is clearly a misunderstanding in the above text. 3DNA/DSSR can handle left-handed Z-DNA without any issues. DSSR also reports negative twist angles for left-handed G4s, as shown clearly for PDB entry 7d5e, for example.

3DNA/DSSR derives a complete of set of six base-pair parameters (including shear and opening), six step parameters (including twist and rise), and six helical parameters, using a rigorously defined and completely reversible algorithm (CEHS) and the standard base-reference frame. See section "3.2.3 Base pairs" in DSSR User Manual for more details. The DSSR output for G4s (as in DSSR-G4DB) reports only twist and rise, along with overlapped areas, simply because these are the most important parameters and easily interpretable.

The list of the resolved G4 structures was downloaded from the ONQUADRO website (https://onquadro.cs.put.poznan.pl/) (39) at about the end of October 2023. It consisted of 291 intramolecular structures (named unimolecular in the website) and 154 intermolecular G4s (96 bimolecular and 58 tetramolecular). Only the intramolecular structures were kept for this study. To this list, we added 55 missing intramolecular structures that were found on the website of DSSR-G4DB (http://g4.x3dna.org) (40). From the merged list, 345 structures were downloaded from the Protein Data Bank (PDB) (http://www.rscb.org/pdb/) (41) because one structure had no available coordinates in the PDB format (7ZJ5 (42)). -- Farag and Mouawad (2024)

DSSR adopts the frame of reference of Webba da Silva, designating the four strands and grooves of G4-stem as shown below using PDB entries 8ht7 (G1 in syc) and 5ua3 (G1 in anti) as example for the syn or anti glycosidic bond of the 5'-guanosine, respectively.

G4 frame of references

In DSSR, the first strand (#1) is always upward (U) from 5' to 3'-end, and the polarity of the other three strands is determined by its orientation relative to #1: U if parallel, or D if antiparallel. There are a total of 2x2x2=8 possible combinations of U and D for the three strands, which define parallel (U4: UUUU), antiparallel (U2D2: UDDU, UDUD, UUDD), or hybrid (UD3: UDDD; U3D: UDUU, UUDU, UUUD). For example, the PDB entry 2lod is characterized by DSSR as:  "hybrid-(mixed), UUUD, U3D(3+1)", and PDB entry 8ht7 as:  "anti-parallel, UDUD, chair(2+2)". This notation is topologically equivalent to the one adopted by ASC-G4 but with opposite orientation of the strands.

Overall, DSSR and ASC-G4 provide different perspectives on G4 structures. It is to the user to decide which one is more suitable for their needs.


References

Farag,M. et al. (2023) ASC-G4, an algorithm to calculate advanced structural characteristics of G-quadruplexes. Nucleic Acids Res., 51, 2087–2107.

Farag,M. and Mouawad,L. (2024) Comprehensive analysis of intramolecular G-quadruplex structures: furthering the understanding of their formalism. Nucleic Acids Res., gkae182.

Comment

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G-quadruplex -- notes on the Webba da Silva nomenclature

In late September of 2018, I contacted Dr. Mateus Webba da Silva requesting a copy of his 2007 article, titled "Geometric formalism for DNA quadruplex folding". At that time, I had implemented a G4 module within DSSR for the automatic identification, comprehensive annotation, and schematic visualization of G-quadruplexes from 3D atomic coordinates. I noticed the 2007 paper, and was intrigued by the following sentences in the abstract:

A formalism is presented describing the interdependency of a set of structural descriptors as a geometric basis for folding of unimolecular quadruplex topologies. It represents a standard for interpretation of structural characteristics of quadruplexes, and is comprehensive in explicitly harmonizing the results of published literature with a unified language.

Mateus kindly sent me a copy of the 2007 article, and shortly afterwards he also shared with me the Dvorkin et al. (2018) paper on "Encoding canonical DNA quadruplex structure". I carefully read both papers, plus the Karsisiotis et al. (2013) tutorial paper. I was impressed by the elegance of the formalism: simple and systematic, so I immediately decided to add this feature to the G4 module of DSSR.

As the Chinese saying goes, "纸上得来终觉浅,绝知此事要躬行" ("What you learn from books is always shallow. You must practice it yourself to know it well." -- Google Translate). The implementation process was challenging because of subtleties in the formalism, but very rewarding. It is all about scientific understanding and software engineering. Only after a thorough understanding and attention to meticulous details can one create a robust and reliable software tool. On the other hand, once properly implemented, the DSSR G4 module can be applied consistently. Any discrepancies between DSSR output and literature merit further investigation. These discrepancies could either arise from bugs in DSSR (which I will promptly address upon identification) or, more likely, typos or errors in the reported results.

Webba da Silva (2007) systematically described the interdependency of glycosidic bond (syn or anti), strand polarity (parallel or anti-parallel), groove width (narrow, medium, or wide), and loop type (lateral, propeller, or diagonal) in unimolecular G-quadruplexes. Figures 1-3 and Scheme 1 of Webba da Silva (2007) are very informative, and easy to follow conceptually. The Karsisiotis et al. (2013) tutorial provided further details based on experimentally determined G-quadruplex structures from the PDB (e.g., Figure 3: the schematic for all possible combinations of glycosidic bond and the corresponding groove-width combinations in G-tetrad). Some key observations:

  • Since glycosidic bond can be either syn or anti, there a total of 2x2x2x2 = 16 possible combinations in a G-tetrad.
  • The disposition of glycosidic bond of guanosines in a G-tetrad leads to only eight possible groove-width combinations.
  • Only tetrads with the same groove-width combinations may stack to form stable G-quadruplexes.
  • Propeller loops invariably link medium grooves within a G-quadruplex stem.
  • Lateral and diagonal loops bridge guanosines of different glycosidic bond.
  • If a single-stranded quadruplex starts with a narrow groove, it can only be with a clockwise loop progression (i.e., +lateral).
  • There are 26 permissible looping combinations within a canonical unimolecular G-quadruplex (G4-stem).

To unambiguously characterize a G4-stem, Webba da Silva (2007) defined a frame of reference where the 5’-G in a G4-stem is set as the origin, and the first strand is progressing towards the viewer. Regardless of the clockwise or anti-clockwise progression of the base sequence, the scheme designates one orientation for the syn and anti glycosidic bond by following G+G H-bonding alignments. Put another way, grooves and strands are strictly related to the reference (first) strand in an anti-clockwise manner, irrespective of the progression of the base sequence. The point is illustrated in the figure below, using PDB entries 8ht7 (G1 in syc) and 5ua3 (G1 in anti) as an example for the syn or anti glycosidic bond of the 5'-guanosine, respectively.

G4 frame of references

Based on previous work, the Dvorkin et al. (2018) paper proposed a systematic nomenclature for G4-stem. The single structural descriptor contains:

  • The number of G-tetrads (i.e., the G-tract length).
  • Loop types (lowercase l for lateral, p for propeller, and d for diagonal) and relative direction ("+" for clockwise and "-" for anti-clockwise progression, using the frame of reference described above).
  • For lateral loops, the groove widths ("w" for wide, and “n” for narrow) are denoted in subscript.

So a complete descriptor could be 2(+lnd−p), as shown in Figure 1A of the Dvorkin et al. (2018) paper. Significantly, Figure 1B therein further gave structural descriptors for six experimentally determined G4-stems from the PDB. These examples, plus the ones in the supplementary materials, were used to validate my implementation of the systematic nomenclature in the G4 module of DSSR. My results agree with those in the Dvorkin et al. (2018) paper, except for two cases, which are discussed below.

  • For PDB entry 2gku: 3(-p-ln-lw) (Dvorkin et al.) vs 3(-P-Lw-Ln) (DSSR), with swapped n (narrow) and w (wide) groove widths for both lateral loops.
  • For PDB entry 2lod: 3(-pd+ln) (Dvorkin et al.) vs 3(-PD+Lw) (DSSR), with swapped n (narrow) and w (wide) groove width for the lateral loop.

Note that in DSSR, I am using uppercase L/P/D for lateral/propeller/diagonal loop types, and lowercase n/w for narrow/wide groove widths, respectively. Doing so distinguishes between the different loop types and groove widths in pure text format.

After careful examination of these discrepancies, I still couldn’t find any errors in my implementation. So I contacted Mateus for verification (in early October 2018). Thankfully, he quickly responded and acknowledged the mistakes for PDB entry 2gku in Dvorkin et al. (2018), saying "There can not be a –Ln after the –p." Clearly, the wrong descriptor for PDB entry 2gku in Dvorkin et al. (2018) was due to a typographical error. This example illustrates the power of a robust software tool like DSSR.


References

Dvorkin,S.A. et al. (2018) Encoding canonical DNA quadruplex structure. Sci. Adv., 4, eaat3007.

Karsisiotis,A.I. et al. (2013) DNA quadruplex folding formalism – A tutorial on quadruplex topologies. Methods, 64, 28–35.

Webba da Silva,M. (2007) Geometric formalism for DNA quadruplex folding. Chemistry A European J, 13, 9738–9745.

Comment

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G-quadruplex -- notes on ElTetrado and related tools

Over the past few years, the Szachniuk group has made several significant contributions to the field of structural bioinformatics of G-quadruplexes. The following five publications are particularly noteworthy, and I am glad to see that 3DNA/DSSR have been cited in all of them.

1. Zok et al. (2020) -- ElTetrado: a tool for identification and classification of tetrads and quadruplexes

The BMC Bioinformatics paper introduced the ElTetrado software tool for identifying and classifying G-tetrads in unimolecular G-quadruplex structures into ONZ taxonomy. Here DSSR is employed to identify base-pairs and base-stacking interactions.

ElTetrado processes PDB and mmCIF files to identify quadruplexes and their component tetrads in nucleic acid structures (Fig. 2). It applies DSSR [24] to collect the preliminary information about base pairs and stacking.

We recommend that, apart from ElTetrado, the users should download the DSSR binary [24] and place it in the same local directory. DSSR is utilized for the preliminary analysis of base pairs in the input 3D structure. Its local installation allows the users to control DSSR execution. For example, one can decide to pass --symmetry parameter to x3dna-dssr binary when dealing with X-ray structures, which is necessary for some quadruplexes.

As documented in the DSSR Manual, by default, DSSR reads in the first model of an NMR ensemble. A biological unit of X-ray crystal structures in the PDB may contain symmetry-related components formatted as a MODEL/ENDMDL delimited, NMR-like ensemble. In such cases, the --symmetry (or --symm) option is required for DSSR to process the entire biological unit.

For example, x3dna-dssr -i=4ms9.pdb1 --symm leads to the identification of 10 Watson-Crick base pairs in the biological unit of PDB entry 4ms9 (uploaded). The --symm option is now enabled for user-uploaded PDB files on the skmatic.x3dna.org website. Without the --symm option, DSSR would not find any Watson-Crick base pairs in 4ms9.pdb1 since MODEL#1 is single stranded.

Noticing the confusion users may have in using the --symm option, I have revised DSSR to check for overlapped residues. When all models in an NMR ensemble are taken as a whole with the --symm option, there will be overlapped residues. In such cases, DSSR will report a diagnostic message and proceed with the first model only. The final result is as if --symm has not been specified. Put another way, specifying --symm for an NMR ensemble does no harm to the analysis. For example, analyzing PDB entry 8xeq with the --symm option would have the following message and only the first model would be processed.

x3dna-dssr -i=8xeq.pdb --symm -o=8xeq.out
[i] You specified --symm, but the input file is an (NMR) ensemble
    *** in the following, only the FIRST model will be processed ***

Alternatively, if the users do not want to have a local version of DSSR binary, they can obtain the DSSR output in JSON format from any place and use them as input data for ElTetrado (with --dssr-json parameter).

ElTetrado is started from the command line. The users enter the program name and either --pdb followed by an input file name (the file should be in PDB or mmCIF format), or --dssr-json followed by a path to JSON file generated by DSSR, or both switches at once.

The JSON output from DSSR can be obtained directly from the skmatic.x3dna.org website for pre-processed PDB entries or user-supplied coordinate files. For examples, for PDB entry 1ehz, the URL is http://skmatic.x3dna.org/pdb/1ehz/1ehz.json. Alternatively, users can use the web API to get the JSON file, as shown below:

# Pre-processed PDB entry:
curl http://skmatic.x3dna.org/api/pdb/1ehz/json

# With user-supplied PDB file
curl http://skmatic.x3dna.org/api -F 'model=@1ehz.pdb' -F 'type=json'
curl http://skmatic.x3dna.org/api -F 'url=https://files.rcsb.org/download/1ehz.pdb.gz' -F 'type=json'

2. Popenda et al. (2020) -- Topology-based classification of tetrads and quadruplex structures

This paper presents the ONZ scheme to clarify tetrads in unimolecular structures (see Figure 2 therein). Note that DSSR, with option --G4=ONZ, classifies G-tetrads into ONZ taxonomy. For example, the PDB entry 2gku has one G-tetrad (G3, G9, G17, G21) in the O- category, and two G-tetrads in O+.

Structures from both sets were analyzed using self-implemented programs along with DSSR software from the 3DNA suite (Lu et al., 2015). From DSSR, we acquired the information about base pairs and stacking.

3. Zurkowski et al. (2022) -- DrawTetrado to create layer diagrams of G4 structures

DrawTetrado generates static layer diagrams that represent structural data in a pseudo-3D perspective. The layer diagram is very informative and visually pleasing, and it complements the cartoon block schematics generated by the DSSR-PyMOL integration and the detailed DSSR characterization of G-quadruplexes.

So far, the only visual model designed for the 3D structure of quadruplexes is cartoon block schematics (Fig. 1C). These models are generated by DSSR-PyMOL integration and presented as static images of the structure viewed from six perspectives (Lu, 2020).

4. Adamczyk et al. (2023) -- WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures

The topologies underlying the classification of quadruplexes and other parameters of their structures can be analyzed using a few computational tools. DSSR (7) was the first to target the detection of G-quadruplexes in 3D structure data saved in PDB and PDBx/mmCIF files and to describe their features. It runs systematically on all entries in the Protein Data Bank and collects motifs found in the DSSR-G4DB database. ElTetrado (8) can identify and analyze G4s and other kinds of tetrads and quadruplexes, classify them, and compute their parameters. It is the core of the computation pipeline running within the ONQUADRO database system (9). The most recent tool for processing atom coordinates in the search for quadruplexes is ASC-G4 (10). It calculates more features than DSSR and ElTetrado, but is limited to unimolecular quadruplexes and supports only the PDB format.

The example illustration in Figure 3 of the paper is on PDB entry 6h1k, the major G-quadruplex form of HIV-1 LTR (long terminal repeat). The layer diagram shown below, re-generated using the WebTetrado website, helps visualize the detailed characterization of DSSR very nicely.

Layer diagram of PDB entry 6h1k "In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, and may contain more than one G4-stem." For PDB entry 6h1k, DSSR identifies a G-helix with three G-tetrads, ordered properly. Specifically, strand#1 consists of (G2, G1, and G25), even G1 and G25 are not covalently connected. On the other hand, "In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. Bulges are also allowed along each of the four strands." Thus, the G4-stem is composed of only two G-tetrads, as detailed below.

Stem#1, 2 G-tetrads, 3 loops, INTRA-molecular, UDDD, hybrid-(mixed), 2(D+PX), UD3(1+3)

 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC Z- nts=4 GGGG A.DG1,A.DG20,A.DG16,A.DG27
 2  glyco-bond=-sss sugar=.-.3 groove=w--n WC-->Major Z+ nts=4 GGGG A.DG2,A.DG19,A.DG15,A.DG26
  step#1  mm(<>,outward)  area=12.76 rise=3.47 twist=18.2
  strand#1  U DNA glyco-bond=s- sugar=-. nts=2 GG A.DG1,A.DG2
  strand#2  D DNA glyco-bond=-s sugar=-- nts=2 GG A.DG20,A.DG19
  strand#3  D DNA glyco-bond=-s sugar=-. nts=2 GG A.DG16,A.DG15
  strand#4  D DNA glyco-bond=-s sugar=-3 nts=2 GG A.DG27,A.DG26
  loop#1 type=diagonal  strands=[#1,#3] nts=12 GAGGCGTGGCCT A.DG3,A.DA4,A.DG5,A.DG6,A.DC7,A.DG8,A.DT9,A.DG10,A.DG11,A.DC12,A.DC13,A.DT14
  loop#2 type=propeller strands=[#3,#2] nts=2 GC A.DG17,A.DC18
  loop#3 type=diag-prop strands=[#2,#4] nts=5 GACTG A.DG21,A.DA22,A.DC23,A.DT24,A.DG25

List of 2 non-stem G4-loops (including the two closing Gs)
 1 type=lateral   helix=#1 nts=5 GACTG A.DG21,A.DA22,A.DC23,A.DT24,A.DG25
 2 type=V-shaped  helix=#1 nts=4 GGGG A.DG25,A.DG26,A.DG27,A.DG28

DSSR correctly identifies the 12-nt diagonal loop, containing a canonical duplex stem and a hairpin loop. Notably, the G-tetrad (25-21-17-28) does not belong to the G4-stem because of the broken backbone connectivity between G1 and G25. Instead, the Gs in the G-tetrad (25-21-17-28) become part of the following two loops, which are certainly unconventional yet follow naturally the DSSR definition of G4-stem.

  • The propeller loop, which now includes G17 (part of the G-tetrad), in addition to C18.
  • The unusual diag-prop (diagonal-propeller ) loop, which consists of G21, A22, C23, T24, and G25.

Moreover, DSSR also reports two loops that are not defined by the G4-stem: the V-shaped loop (G25-G26-G27-G28) and the lateral loop (G21-A22-C23-T24-G25). See the notes in the above layer diagram. V-shaped loop occurs when the 5’-endmost G-tetrad lies in the middle of the G-quartets stack as in the non-canonical G4 structures with snapbacks.

The G4-helix and G4-stem definitions parallel those for duplex helix and stem in DSSR. The characterization of loops follows naturally once G4-stem or duplex stem are identified. The unusual propeller and diagonal-propeller loops noted above are due to non-canonical structures, which also lead to the listing of non-stem G4-loops.

I may consider to add special handling of snapbacks (or other worthwhile classes of non-canonical G4 structures) so that the reported loops follow whatever consensus the community agrees upon in the future. Nevertheless, I would like to emphasize that the consistent definitions of G4-stem and loops in DSSR help pinpoint extraordinary features to draw users' attention to non-canonical G4 structures. The layer diagram from DrawTetrado and WebTetrado are very handy in illuminating the basic concept and technical details, as shown here for PDB entry 6h1k.

5. Zok et al. (2022) -- ONQUADRO: a database of experimentally determined quadruplex structures

The computational engine is composed of scripts utilising in-house and third-party procedures, responsible for data collection, quadruplex identification, computation of structure parameters, secondary structure annotation, visualisation of the secondary and tertiary structure models, database queries, generation of statistics, and newsletter preparation. DSSR (--pair-only mode) (36) and ElTetrado (39) functionalities are applied to identify quadruplexes, tetrads, and G4-helices in nucleic acid structures.


References

Adamczyk, B., Zurkowski, M., Szachniuk, M., & Zok, T. (2023). WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures. Nucleic Acids Research, 51(W1), W607–W612. https://doi.org/10.1093/nar/gkad346

Popenda, M., Miskiewicz, J., Sarzynska, J., Zok, T., & Szachniuk, M. (2020). Topology-based classification of tetrads and quadruplex structures. Bioinformatics, 36(4), 1129–1134. https://doi.org/10.1093/bioinformatics/btz738

Zok, T., Kraszewska, N., Miskiewicz, J., Pielacinska, P., Zurkowski, M., & Szachniuk, M. (2022). ONQUADRO: a database of experimentally determined quadruplex structures. Nucleic Acids Research, 50(D1), D253–D258. https://doi.org/10.1093/nar/gkab1118

Zok, T., Popenda, M., & Szachniuk, M. (2020). ElTetrado: a tool for identification and classification of tetrads and quadruplexes. BMC Bioinformatics, 21(1), 40. https://doi.org/10.1186/s12859-020-3385-1

Zurkowski, M., Zok, T., & Szachniuk, M. (2022). DrawTetrado to create layer diagrams of G4 structures. Bioinformatics, 38(15), 3835–3836. https://doi.org/10.1093/bioinformatics/btac394

Comment

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G-quadruplex -- notes on CIIS-GQ

I recently came across the Direk & Doluca (2024) paper on CIIS‐GQ: Computational Identification and Illustrative Standard for representation of unimolecular G‐Quadruplex secondary structures. Since DSSR is mentioned extensively in this work, with a section comparing CIIS-GQ and DSSR in supplementary materials, it is worthwhile to explore the issues raised in the paper. Overall, following literature allows me to clarify misconceptions and fix bugs that further improve DSSR.

The data which contain the G-quadruplexes were identified by DSSR-G4DB website [12, 13, 16]. All of the PDB (protein data bank) ids of DNA and RNA structures are extracted from the aforementioned website and the pdb files which contain the three dimensional data of the corresponding structures were downloaded from the protein data bank [3–5]. [under section "Materials and Methods": "Data"]

The DNA and RNA structures listed in 3DNA website were identified and downloaded from Protein Data Bank. Only unimolecular structures were used for the rest of the study (Supplementary Fig. 2). [under section "Results"]

Additionally, DSSR requires licensing to get annotation results for G-quadruplex structures. Fortunately, the annotation results for a number of G-quadruplexes were already published at DSSR-G4DB (46) and we were able to compare. [under section "Comparison with DSSR" in supplemental materials]

I am glad the DSSR-G4DB website served as a starting point for this study. The G4.x3dna.org website, where DSSR-G4DB is hosted, has always been available to the public. With the NIH R24GM153869 grant support, the standalone DSSR software is free for academic use and can be obtained from the Columbia Technology Ventures (CTV) website.

All obtained results for each pdb file were compared with DSSR. Out of which 35 DNA and 13 RNA structures were analyzed differently (Supplementary Table 2). Significant differences were detected for a number of structures between CIIS-GQ and DSSR analysis. For example, in 1k8p, 3ibk, 6ip7 and 5ccw structures, DSSR fails to identify some loops in some structures.

Most common issue that we have observed with DSSR is that it places loops in wrong places in some structures. For example, In 2a5p structure, the first loop is identified as reversal by both tools but DSSR also assigns the G6 to this loop which already participates in a tetrad. Such misplacement of tetrad-forming guanines in a loop is also seen in other structures such as 2a5r, 2kpr, 2m53, 2m92, etc (Supplementary Table 2).

The G4 module in DSSR was first developed around 2017-2018 and the work was mentioned briefly in the Lu (2020) paper on DSSR-PyMOL integration. However, due to the funding gap, the development of the G4 module was put on hold. I have never got a chance to write a paper documenting the detailed algorithms for the identification, annotation, and visualization of G-quadruplexes. I recently revamped the G4.x3dna.org website from inside out, and reprocessed all PDB structures to compile the DSSR-G4DB database. Along the way, the G4 module has been updated and improved. Now I'm actively working on a manuscript on the G4 module in DSSR and the associate website.

DSSR has clear definitions of G4-helix and G4-stem, and the corresponding loops. Specifically, for PDB entry 2a5p, DSSR reports the following:

## List of 1 G4-helix

In DSSR, a G4-helix is defined by stacking interactions of G-tetrads, regardless of backbone connectivity, 
and may contain more than one G4-stem.

##### Helix#1, 3 G-tetrads, INTRA-molecular, with 1 stem

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
 2  glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
 3  glyco-bond=-s-- sugar=-3-- groove=wn-- WC-->Major Z- nts=4 GGGG A.DG6,A.DG24,A.DG15,A.DG19
  step#1  pm(>>,forward)  area=9.64  rise=3.19 twist=32.7
  step#2  pm(>>,forward)  area=12.93 rise=3.29 twist=29.4
  strand#1 DNA glyco-bond=--- sugar=-.- nts=3 GGG A.DG4,A.DG5,A.DG6
  strand#2 DNA glyco-bond=--s sugar=--3 nts=3 GGG A.DG8,A.DG9,A.DG24
  strand#3 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG13,A.DG14,A.DG15
  strand#4 DNA glyco-bond=--- sugar=--- nts=3 GGG A.DG17,A.DG18,A.DG19

Notice the differences in grooves between the first two G-tetrads vs the 3rd one, and the breaking backbone for strand#2 between G9 and G24.

## List of 1 G4-stem

In DSSR, a G4-stem is defined as a G4-helix with backbone connectivity. 
Bulges are also allowed along each of the four strands.

##### Stem#1, 2 G-tetrads, 3 loops, INTRA-molecular, UUUU, parallel, 2(-P-P-P), parallel(4+0)

 1  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG4,A.DG8,A.DG13,A.DG17
 2  glyco-bond=---- sugar=.--- groove=---- WC-->Major O+ nts=4 GGGG A.DG5,A.DG9,A.DG14,A.DG18
  step#1  pm(>>,forward)  area=9.64  rise=3.19 twist=32.7
  strand#1  U DNA glyco-bond=-- sugar=-. nts=2 GG A.DG4,A.DG5
  strand#2  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG8,A.DG9
  strand#3  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG13,A.DG14
  strand#4  U DNA glyco-bond=-- sugar=-- nts=2 GG A.DG17,A.DG18
  loop#1 type=propeller strands=[#1,#2] nts=2 GT A.DG6,A.DT7
  loop#2 type=propeller strands=[#2,#3] nts=3 gGA A.DI10,A.DG11,A.DA12
  loop#3 type=propeller strands=[#3,#4] nts=2 GT A.DG15,A.DT16

Thus the G4-stem consists of two G-tetrads only, and G6 which is part of the 3rd G-tetrad becomes part of a propeller loop. Similar arrangement applies to the other cases. 2a5p DSSR also reports the following loop:

## List of 1 non-stem G4-loop (including the two closing Gs)

 1 type=diagonal  helix=#1 nts=6 GGAAGG A.DG19,A.DG20,A.DA21,A.DA22,A.DG23,A.DG24

In my understanding, the definition and nomenclature of loops in G4 structures are not yet standardized. I am monitoring the development in this field and will update DSSR as needed in due course.

There may also be different types of loops identified by these tools. For example, in 1oz8, which is depicted by CIISGQ as two separate G4s, DSSR fails to identify the G-tetrad, [2, 5, 8, 11], that lies on the outside of the structure. This results in identification of loops formed within this tetrad and its stacking neighbor different to CIIS-GQ. While CIISGQ identifies these loops as reversal, just like the other loops in the structure, DSSR identifies them as non-stem lateral loops. This causes complete misinterpretation of the size and the type of loops in the structure.

The revised DSSR output for PDB entry 1oz8 has the G-tetrad A.DG2,A.DG5,A.DG8,A.DG11 manually added as part of the input, and now all three propeller loops are correctly identified. By default, G11 does not form proper G+G pairs (of LW type cWH or cHW, and Saenger type VI) with G2 and G8. The distortion of the G-tetrad is obvious in the block representation of the structure.

In 4u5m, similar to 1oz8, the structure may be interpreted as two separate G4s connected through a single link (T13,T14). In this case, DSSR identifies only two loops in one of the G4s and labels them as non-stem V-shaped loops. This also differs from CIIS-GQ where CIIS-GQ interprets all loops in both G4 as reversal. Structures containing multiple G4s, such as 1oz8, 4u5m and 6kvb, are often identified with different loop types by DSSR, while CIIS-GQ can recognise the loops correctly and simplifies the comprehension of the structure.

For PDB entry 4u5m, the same arguments above regarding the G4-stem and loops for 2a5p apply.

 1  glyco-bond=s--- sugar=---- groove=w--n Major-->WC O+ nts=4 GGGG A.DG2,A.DG11,A.DG8,A.DG5
 2  glyco-bond=---- sugar=---- groove=---- Major-->WC O+ nts=4 GGGG A.DG3,A.DG12,A.DG9,A.DG6
 3  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG24,A.DG15,A.DG18,A.DG21
 4  glyco-bond=---- sugar=---- groove=---- WC-->Major O+ nts=4 GGGG A.DG23,A.DG26,A.DG17,A.DG20

As shown, the backbone between G15 and G26 is broken. Moreover, here the assignment of Gs along the strand may need to be manually adjusted.

As shown in Table 1, by relaxing angle and distance parameters, we were able to identify more tetrads (6T2G, 1OZ8) than DSSR, which detects them as multiplets instead.

The current DSSR results for PDB entry 6t2g and 1oz8 are all as expected. Moreover, DSSR can handle PDB entry 6t2g automatically, while for PDB entry 1oz8 user needs to manually edit the input to include the G-tetrad with G11. By allowing users to specify tetrads, DSSR offers precise control and great flexibility, e.g., to include the G-C-G-C tetrads in PDB entry 1a6h.

DSSR has a detailed explanation of strands, tetrads and loops. However, the comprehensive output of DSSR is often hard to understand and grasp the details of the structure. [in supplemental materials]

The detailed explanations are provided to help users understand the DSSR output. They are most insightful in combination with the schematic block diagrams. For examples, for PDB entry 1a6h, the middle G-C-G-C tetrads are crystal clear with the long green and yellow rectangular blocks, specially along with the detailed annotations of the tetrads, as shown below.

 1  glyco-bond=s-s- sugar=---. groove=wnwn Major-->WC -- nts=4 GGGG A.DG1,A.DG11,B.DG8,B.DG4
 2  glyco-bond=---- sugar=-.-- groove=----     --     -- nts=4 CGCG A.DC2,A.DG10,B.DC9,B.DG3
 3  glyco-bond=---- sugar=--.- groove=----     --     -- nts=4 GCGC A.DG3,A.DC9,B.DG10,B.DC2
 4  glyco-bond=-s-s sugar=---- groove=wnwn WC-->Major -- nts=4 GGGG A.DG4,A.DG8,B.DG11,B.DG1

1a6h

Another advantage of CIIS-GQ is that it requires only two thresholds, the thresholds of distance and angle parameters that can be modified to detect loosely connected tetrads. Due to this advantage, the identification of the tetrads were possible in at least two structures. In case of 1OZ8, DSSR found three tetrads (G1-G4-G7-G10, G13-G16-G19-G22 and G14-G17-G20-G23) as shown at the result page2 (47) while CIIS-GQ has found one more tetrad which is G2-G5-G8-G11. In comparison DSSR highlighted G5-G8-G11 as a multiplet, omitting the G2. Based on this difference, loop classification differs with CIIS-GQ. DSSR has identified 3 stem reversal loops and 3 non-stem lateral loops while we have identified 7 reversal loops. Stem loop is defined as any loop that also forms a duplex within itself.

DSSR now has PDB entry 1oz8 properly characterized, by manually adding the G-tetrad involving G11, as detailed above.

A similar difference exists in 6T2G. DSSR could find 2 tetrads in this structure (G2-G6-G11-G26 and G4-G9-G13-G28) as shown at the result page3 (47) while CIIS-GQ found one more tetrad, G3-G7-G12-G27. DSSR is able to show these four guanines as a multiplet in the list of multiplets section, however does not present it as a tetrad like the other two tetrads. As a result, CIIS-GQ loop types and placements are also different. DSSR has found six lateral loops while CIIS-GQ has found three reversal loops.

DSSR can now handle PDB entry 6t2g automatically. Previous versions of DSSR missed the G-tetrad (G3+G7+G12+G27) because of the G12+G27 pair: it fails the criteria to be classified as the pair of LW type cWH or cHW and Saenger type VI. Thus G3+G7+G12+G27 do not qualify as a G-tetrad, but they still form a multiplet with four guanines.


References

Direk, T., & Doluca, O. (2024). Computational Identification and Illustrative Standard for Representation of Unimolecular G-Quadruplex Secondary Structures (CIIS-GQ). Journal of Computer-Aided Molecular Design, 38(1), 35. https://doi.org/10.1007/s10822-024-00573-1

Lu, X.-J. (2020). DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL. Nucleic Acids Research, gkaa426. https://doi.org/10.1093/nar/gkaa426

Comment

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Torsion angles from DSSR

By following citations to 3DNA/DSSR, I recently came across the paper "RNAtango: Analysing and comparing RNA 3D structures via torsional angles" in PLOS Computational Biology by Mackowiak M, Adamczyk B, Szachniuk M, and Zok T. This work provides a nice summary of definitions of torsion and pseudo-torsion angles in RNA structure, and an angular metrics (MCQ, Mean of Circular Quantities) to score structure similarity. The RNAtango web application allows user to explore the distribution of torsion angles in a single structure/fragment (Single model), compare RNA models with a native structure (Models vs Target), or perform a comparative analysis in a set of models (Model vs Model).

In the Introduction section, 3DNA/DSSR are mentioned along with other related tools, as below:

Several bioinformatics tools have been designed for analyzing torsion and pseudotorsion angles, each with its own strengths and limitations. 3DNA, an open-source toolkit, provides comprehensive functionality, including torsion and pseudotorsion angle calculations [27], but lacks support for the current standard PDBx/mmCIF file format. DSSR, the successor to 3DNA, overcomes this limitation by supporting both PDB and PDBx/mmCIF files. However, it is a closed-source, commercial application that requires licensing, even for research purposes [28]. Curves+, another tool used for torsion angle analysis, is currently inaccessible due to the unavailability of its webpage and source code hosting [29]. Barnaba, a Python library and toolset for analyzing single structures or trajectories, supports torsion angle calculations but, like 3DNA, does not support the PDBx/mmCIF format [30]. For users seeking a more user friendly option, AMIGOS III offers a PyMOL plugin that calculates pseudotorsion angles and presents them in Ramachandran-like plots [17].

Every bioinformatic software has been developed for a specific purpose, and no two such tools can be identical. It is a good thing that the community has a choice for RNA backbone analysis. Indeed, 3DNA has been superseded by DSSR, which is licensed by Columbia Technology Ventures (CTV) to ensure its continuous development and availability. However, DSSR remain competitive due to its unmatched functionality, usability, and support: it saves users a substantial amount of time and effort when compared to other options.

From the very beginning, it has been my dream to make DSSR stand out for its quality and value, and be widely accessible. The CTV DSSR distribution by no means follow typical commercial license for a software product: specifically, it does not include a license key to limit DSSR's usage to a specific machine and operating system, and there is no expire date for the software either. Moreover, the Basic Academic license was free of charge when DSSR was initially licensed by the CTV in August 2020, and remained so until around end of 2021 when the web-based "Express Licenses" functionality no longer worked. Manually handling the large number of requests for free academic licenses was not sustainable, and that was when the DSSR Basic Academic free license was removed. Upon user requests, we late on re-introduced DSSR Basic Academic license, but with a one-time fee of $200 to cover the running cost. That may be reason for the remark in the RNAtango paper that DSSR "requires licensing, even for research purposes".

With the recent NIH R24 funding support on "X3DNA-DSSR: a resource for structural bioinformatics of nucleic acids", we are providing DSSR Basic free of charge to the academic community. Academic Users may submit a license request for DSSR Basic or DSSR Pro by clicking "Express Licensing". Checking the list of licensees, I am thrilled to see the many new DSSR users from leading institutions around the world, including Stockholm University, Ghent University, Universitaet Heidelberg, University of Palermo, CSSB-Hamburg, Nicolaus Copernicus University, NIH, Harvard, ... Clearly, DSSR fills a niche, and the demands for it remain strong!

Back to torsion angles, it is safe to say that DSSR has unique features not available or easily accessible elsewhere. Here are some use cases using tRNA PDB entry 1ehz as an example:

x3dna-dssr -i=1ehz.cif # generate dssr-torsions.txt among other output files
x3dna-dssr -i=1ehz.cif --torsion-file -o=1ehz-torsions.txt # just the torsion file 1ehz-torsions.txt
x3dna-dssr -i=1ehz.cif --json | jq .nts[54] > 1ehz-PSU55.txt # DSSR-derived features for nucleotide PSU55

Users can easily run the DSSR commands listed above and get the results in human-readable text and machine-friendly JSON formats. For verification, the contents of 1ehz-torsions.txt and 1ehz-PSU55.txt are available by clicking the links.

It is worth noting that DSSR has the --nmr option for the analysis of an ensemble of NMR structures, in .pdb or .cif format, as deposited in the PDB. The combination of --nmr and --json renders DSSR easily accessible to the molecular dynamics (MD) community.

In principle, calculating torsion angles is a straightforward process. In reality, factors such as modified nucleotides (especially pseudouridine), missing atoms, NMR ensembles or MD trajectories, PDB vs mmCIF formats, etc. make the implementation complicated. Without paying great attention to details, it is easy to make subtle mistakes. For example, with RNAtango the chi (χ) torsion angle for A.PSU55 of 1ehz is listed as -152.42°, which is wrong. The correct value should be -147.0° as reported by DSSR (see below and the link 1ehz-PSU55.txt above).

DSSR provides a comprehensive list of backbone parameters (as listed below for 1ehz). The program is efficient and robust, and has been battle tested. I am always quick to fix any bugs once verified, and am willing to add new features once thoroughly studied. In short, DSSR has been designed to be a reliable tool that the community can trust and build upon.


DSSR-derived backbone features for tRNA 1ehz:

         Output of DNA/RNA backbone conformational parameters
             DSSR v2.4.5-2024sep24 by xiangjun@x3dna.org
******************************************************************************************
Main chain conformational parameters:

  alpha:   O3'(i-1)-P-O5'-C5'
  beta:    P-O5'-C5'-C4'
  gamma:   O5'-C5'-C4'-C3'
  delta:   C5'-C4'-C3'-O3'
  epsilon: C4'-C3'-O3'-P(i+1)
  zeta:    C3'-O3'-P(i+1)-O5'(i+1)
  e-z:     epsilon-zeta (BI/BII backbone classification)

  chi for pyrimidines(Y): O4'-C1'-N1-C2; purines(R): O4'-C1'-N9-C4
    Range [170, -50(310)] is assigned to anti, and [50, 90] to syn

  phase-angle: the phase angle of pseudorotation and puckering
  sugar-type: ~C2'-endo for C2'-endo like conformation, or
               ~C3'-endo for C3'-endo like conformation
              Note the ONE column offset (for easy visual distinction)

ssZp: single-stranded Zp, defined as the z-coordinate of the 3' phosphorus atom
      (P) expressed in the standard reference frame of the 5' base; the value is
      POSITIVE when P lies on the +z-axis side (base in anti conformation);
      NEGATIVE if P is on the -z-axis side (base in syn conformation)
  Dp: perpendicular distance of the 3' P atom to the glycosidic bond
      [Ref: Chen et al. (2010): "MolProbity: all-atom structure
            validation for macromolecular crystallography."
            Acta Crystallogr D Biol Crystallogr, 66(1):12-21]
splay: angle between the bridging P to the two base-origins of a dinucleotide.

          nt               alpha    beta   gamma   delta  epsilon   zeta     e-z        chi            phase-angle   sugar-type    ssZp     Dp    splay
 1     G A.G1                ---  -128.1    67.8    82.9  -155.6   -68.6    -87(BI)   -167.8(anti)    16.1(C3'-endo)  ~C3'-endo    4.59    4.57   24.92
 2     C A.C2              -67.4  -178.4    53.8    83.4  -145.1   -76.8    -68(BI)   -163.8(anti)    16.1(C3'-endo)  ~C3'-endo    4.52    4.63   21.15
 3     G A.G3              -74.5   169.7    59.5    80.7  -148.3   -80.0    -68(BI)   -161.9(anti)    14.6(C3'-endo)  ~C3'-endo    4.75    4.69   22.28
 4     G A.G4              -64.4   162.2    60.7    82.2  -157.4   -68.7    -89(BI)   -168.7(anti)    20.8(C3'-endo)  ~C3'-endo    4.68    4.57   25.22
 5     A A.A5              -74.7  -176.5    53.4    84.9  -137.5   -81.7    -56(BI)   -162.9(anti)     4.8(C3'-endo)  ~C3'-endo    4.49    4.76   22.04
 6     U A.U6              -48.8   157.6    55.3    81.3  -151.0   -77.0    -74(BI)   -160.0(anti)    18.2(C3'-endo)  ~C3'-endo    4.31    4.51   22.89
 7     U A.U7              -59.5  -178.7    62.5   137.3  -105.9   -52.0    -54(--)   -133.1(anti)   156.1(C2'-endo) ~C2'-endo     1.55    1.41  126.99
 8     U A.U8              -83.8  -145.6    55.4    78.6  -142.8  -118.6    -24(--)   -161.5(anti)    10.5(C3'-endo)  ~C3'-endo    4.60    4.76   62.37
 9     A A.A9              -69.7  -141.7    52.3   147.8  -106.2   -77.3    -29(--)    -70.5(anti)   149.8(C2'-endo) ~C2'-endo     1.00    1.14   57.38
 10    g A.2MG10           177.8   147.2    60.1    89.3  -126.2   -88.7    -37(--)    169.6(anti)     6.6(C3'-endo)  ~C3'-endo    4.68    4.63   23.87
 11    C A.C11             -56.1   167.9    48.2    87.2  -150.5   -69.9    -81(BI)   -160.9(anti)    16.8(C3'-endo)  ~C3'-endo    4.28    4.46   21.20
 12    U A.U12             -67.8   172.9    51.8    80.7  -158.5   -65.2    -93(BI)   -158.3(anti)    25.2(C3'-endo)  ~C3'-endo    4.29    4.45   21.01
 13    C A.C13             166.6  -169.9   178.6    82.5  -153.1   -97.4    -56(BI)   -168.3(anti)    23.7(C3'-endo)  ~C3'-endo    4.28    4.36   31.59
 14    A A.A14              83.4  -158.3  -114.6    92.0  -125.5   -57.3    -68(--)   -170.7(anti)   358.9(C2'-exo)   ~C3'-endo    4.67    4.74   38.01
 15    G A.G15             -55.1   162.5    51.9    79.8  -136.3  -143.9      8(--)   -164.5(anti)    16.0(C3'-endo)  ~C3'-endo    4.72    4.74   26.17
 16    u A.H2U16            -6.1    91.2    76.8    96.8   -61.8  -131.2     69(--)    -85.8(anti)    18.8(C3'-endo)  ~C3'-endo   -0.71    3.38  145.77
 17    u A.H2U17            27.8   107.7   174.1    94.8   178.0    76.2    102(--)   -142.5(anti)   341.4(C2'-exo)   ~C3'-endo   -0.90    4.20  105.55
 18    G A.G18              45.4  -159.4    59.0   150.6   -95.2  -179.1     84(BII)   -99.5(anti)   154.3(C2'-endo) ~C2'-endo     1.60    1.09   51.64
 19    G A.G19             -71.4  -178.9    53.8   153.8   -91.6   -83.7     -8(--)    -80.3(anti)   167.6(C2'-endo) ~C2'-endo    -1.14    0.48  130.30
 20    G A.G20             -81.3  -150.7    47.8    89.9  -122.3   -54.1    -68(--)    177.8(anti)     8.7(C3'-endo)  ~C3'-endo    4.90    4.76   57.04
 21    A A.A21             -75.6   148.6  -176.6    78.2  -168.9   -75.6    -93(BI)   -160.2(anti)    13.0(C3'-endo)  ~C3'-endo    4.00    4.26   40.66
 22    G A.G22             158.8   153.5   179.3    82.0  -145.0   -80.4    -65(BI)   -175.5(anti)   353.8(C2'-exo)   ~C3'-endo    4.60    4.73   25.62
 23    A A.A23             -53.3   174.8    52.5    82.3  -155.3   -66.4    -89(BI)   -158.0(anti)    12.6(C3'-endo)  ~C3'-endo    4.18    4.61   22.96
 24    G A.G24             -68.8   178.2    46.8    83.6  -144.3   -72.8    -71(BI)   -160.7(anti)    13.4(C3'-endo)  ~C3'-endo    4.63    4.74   20.51
 25    C A.C25             -65.1   168.9    53.9    83.3  -145.1   -68.4    -77(BI)   -160.3(anti)    17.4(C3'-endo)  ~C3'-endo    4.56    4.70   30.70
 26    g A.M2G26           -53.8   170.8    47.7    86.0  -136.3   -76.9    -59(BI)   -163.4(anti)     9.3(C3'-endo)  ~C3'-endo    4.57    4.67   27.36
 27    C A.C27             -53.0   166.9    43.6    83.4  -148.5   -73.4    -75(BI)   -168.2(anti)    18.3(C3'-endo)  ~C3'-endo    4.53    4.62   23.07
 28    C A.C28             -72.4   178.3    49.3    80.1  -152.1   -67.0    -85(BI)   -160.6(anti)     9.2(C3'-endo)  ~C3'-endo    4.55    4.73   21.61
 29    A A.A29             -66.6   174.0    55.6    81.4  -155.5   -78.3    -77(BI)   -165.9(anti)    13.7(C3'-endo)  ~C3'-endo    4.73    4.65   26.96
 30    G A.G30             -54.0   165.9    56.9    83.6  -144.7   -62.3    -82(BI)   -171.7(anti)    14.5(C3'-endo)  ~C3'-endo    4.67    4.65   25.72
 31    A A.A31             -69.9   177.8    52.3    83.7  -137.0   -75.5    -61(BI)   -156.7(anti)    14.6(C3'-endo)  ~C3'-endo    4.24    4.72   21.52
 32    c A.OMC32           -52.7   161.4    49.3    80.1  -145.9   -71.2    -75(BI)   -149.9(anti)    20.4(C3'-endo)  ~C3'-endo    4.16    4.63   25.94
 33    U A.U33             -67.7  -177.0    47.0    82.1  -148.0   -53.7    -94(BI)   -148.2(anti)    13.3(C3'-endo)  ~C3'-endo    4.19    4.64   75.47
 34    g A.OMG34           171.1   148.1    52.5    83.4  -132.5   -71.8    -61(BI)   -171.2(anti)    12.2(C3'-endo)  ~C3'-endo    4.15    4.58   22.09
 35    A A.A35             -47.7   163.7    40.2    80.9  -143.7   -59.5    -84(BI)   -154.4(anti)    21.9(C3'-endo)  ~C3'-endo    4.20    4.54   20.57
 36    A A.A36             -52.4   165.7    51.3    72.2  -160.4   -85.2    -75(BI)   -158.4(anti)    45.8(C4'-exo)   ~C3'-endo    4.49    4.31   24.48
 37    g A.YYG37           -57.5   163.0    47.8    81.1  -148.1   -67.0    -81(BI)   -168.8(anti)    15.4(C3'-endo)  ~C3'-endo    4.63    4.65   32.08
 38    A A.A38             -61.8  -180.0    46.9    82.5  -136.8   -76.4    -60(BI)   -169.4(anti)     2.4(C3'-endo)  ~C3'-endo    4.63    4.78   23.75
 39    P A.PSU39           -47.7   160.4    53.3    79.3  -140.1   -68.6    -72(BI)   -165.6(anti)    15.8(C3'-endo)  ~C3'-endo    4.55    4.68   26.68
 40    c A.5MC40           -67.4   172.0    56.2    83.2  -154.2   -74.9    -79(BI)   -162.6(anti)    17.3(C3'-endo)  ~C3'-endo    4.52    4.60   27.71
 41    U A.U41             -68.2  -179.4    52.4    78.9  -137.3   -84.7    -53(BI)   -169.0(anti)    13.4(C3'-endo)  ~C3'-endo    4.54    4.75   24.14
 42    G A.G42             -47.9   158.7    55.6    79.8  -160.3   -70.3    -90(BI)   -169.0(anti)    20.9(C3'-endo)  ~C3'-endo    4.43    4.51   23.54
 43    G A.G43             -67.0  -178.3    55.6    81.6  -154.9   -76.4    -78(BI)   -160.2(anti)    12.6(C3'-endo)  ~C3'-endo    4.24    4.61   20.95
 44    A A.A44             -59.7   162.1    60.0    85.3  -142.8   -57.2    -86(BI)   -159.4(anti)    16.9(C3'-endo)  ~C3'-endo    4.25    4.61   31.07
 45    G A.G45             -71.9  -176.9    51.0    87.6  -135.1   -78.7    -56(BI)   -149.3(anti)    15.4(C3'-endo)  ~C3'-endo    4.01    4.58   40.27
 46    g A.7MG46           -56.8  -146.5    48.4   141.6  -102.7  -137.9     35(--)    -65.8(anti)   154.5(C2'-endo) ~C2'-endo     0.21    0.96  139.04
 47    U A.U47              62.4  -164.0    44.4   146.1   -93.7   -78.0    -16(--)   -112.0(anti)   164.9(C2'-endo) ~C2'-endo     0.26    0.39  157.37
 48    C A.C48             -73.5  -174.3   161.5   145.6  -143.5    75.6    141(--)   -140.1(anti)   158.2(C2'-endo) ~C2'-endo     1.92    1.80  147.54
 49    c A.5MC49            50.7   168.5    42.2    84.3  -145.0   -82.1    -63(BI)   -173.6(anti)    10.1(C3'-endo)  ~C3'-endo    4.77    4.75   25.83
 50    U A.U50             -51.7   177.2    42.1    80.4  -150.6   -67.8    -83(BI)   -165.3(anti)     5.6(C3'-endo)  ~C3'-endo    4.38    4.75   23.15
 51    G A.G51             -63.9   176.8    52.8    79.4  -150.4   -71.3    -79(BI)   -156.6(anti)    11.5(C3'-endo)  ~C3'-endo    4.44    4.67   21.28
 52    U A.U52             -64.7   173.6    48.5    80.3  -156.5   -69.4    -87(BI)   -164.0(anti)    14.1(C3'-endo)  ~C3'-endo    4.64    4.74   25.47
 53    G A.G53             -56.9   171.5    56.2    83.9  -159.4   -64.9    -95(BI)   -169.2(anti)    19.8(C3'-endo)  ~C3'-endo    4.59    4.57   24.53
 54    t A.5MU54           -79.7  -172.8    57.7    77.6  -128.6   -70.7    -58(BI)   -161.5(anti)    20.6(C3'-endo)  ~C3'-endo    4.56    4.80   30.73
 55    P A.PSU55           -49.7   168.8    44.1    76.6  -140.8   -69.9    -71(BI)   -147.0(anti)    10.1(C3'-endo)  ~C3'-endo    4.15    4.74   71.28
 56    C A.C56             166.4   171.8    53.3    83.4  -132.7   -70.6    -62(BI)   -161.5(anti)    12.6(C3'-endo)  ~C3'-endo    4.37    4.76   28.07
 57    G A.G57             -65.7   167.1    57.5    81.7  -145.2   -67.6    -78(BI)   -159.3(anti)    12.8(C3'-endo)  ~C3'-endo    4.36    4.65   42.47
 58    a A.1MA58           -60.8  -146.1    71.8   156.7   -78.3  -169.3     91(BII)   -86.3(anti)   161.1(C2'-endo) ~C2'-endo     0.48    0.68   73.92
 59    U A.U59              72.6  -158.8    63.7    84.6  -148.8   -53.7    -95(BI)   -165.6(anti)    25.8(C3'-endo)  ~C3'-endo    4.67    4.42   27.88
 60    C A.C60             -72.2   179.5    66.0   148.3   -97.1   -66.4    -31(--)   -117.8(anti)   154.8(C2'-endo) ~C2'-endo     0.99    0.86   90.64
 61    C A.C61             -84.3   179.8    38.2    83.0  -152.3   -74.5    -78(BI)   -166.7(anti)    14.8(C3'-endo)  ~C3'-endo    4.45    4.52   25.80
 62    A A.A62             -60.1   179.6    46.9    80.5  -145.6   -74.1    -71(BI)   -158.7(anti)     9.9(C3'-endo)  ~C3'-endo    4.18    4.66   19.23
 63    C A.C63             -62.0   167.3    50.9    80.7  -152.3   -70.7    -82(BI)   -152.6(anti)    10.7(C3'-endo)  ~C3'-endo    4.32    4.62   23.62
 64    A A.A64             -66.9   180.0    44.1    75.8  -147.5   -76.5    -71(BI)   -161.8(anti)    12.9(C3'-endo)  ~C3'-endo    4.68    4.86   25.64
 65    G A.G65             -44.0   164.2    49.9    79.8  -152.0   -73.3    -79(BI)   -172.8(anti)    16.5(C3'-endo)  ~C3'-endo    4.92    4.76   25.20
 66    A A.A66             -57.9   178.5    52.0    81.7  -151.0   -73.5    -77(BI)   -164.9(anti)    22.5(C3'-endo)  ~C3'-endo    4.56    4.60   22.73
 67    A A.A67             -62.0   164.1    54.2    83.2  -152.2   -78.3    -74(BI)   -162.8(anti)    15.0(C3'-endo)  ~C3'-endo    4.71    4.67   23.30
 68    U A.U68             -59.8   175.3    47.3    82.2  -152.9   -65.4    -88(BI)   -160.1(anti)    11.2(C3'-endo)  ~C3'-endo    4.30    4.60   24.35
 69    U A.U69             -63.8   168.1    55.1    79.1  -155.4   -85.6    -70(BI)   -161.4(anti)    14.7(C3'-endo)  ~C3'-endo    4.55    4.61   19.23
 70    C A.C70             -61.7   164.6    53.1    79.0  -158.5   -64.5    -94(BI)   -152.0(anti)    15.0(C3'-endo)  ~C3'-endo    4.20    4.56   20.96
 71    G A.G71             -78.4   173.6    60.3    80.3  -149.6   -68.4    -81(BI)   -162.8(anti)    13.5(C3'-endo)  ~C3'-endo    4.50    4.71   22.80
 72    C A.C72             -73.2   176.2    62.1    83.0  -152.3   -67.9    -84(BI)   -161.6(anti)    19.5(C3'-endo)  ~C3'-endo    4.56    4.63   26.14
 73    A A.A73             -63.3   177.7    50.4    81.6  -148.2   -66.1    -82(BI)   -167.4(anti)    15.0(C3'-endo)  ~C3'-endo    4.65    4.71   26.33
 74    C A.C74             -66.9  -174.9    50.7    85.9  -145.0   -58.8    -86(BI)   -153.1(anti)    11.8(C3'-endo)  ~C3'-endo    4.22    4.61   33.45
 75    C A.C75             -52.3   175.7    42.3    85.6  -131.9   163.9     64(BII)  -151.7(anti)    15.1(C3'-endo)  ~C3'-endo    3.96    4.60  159.78
 76    A A.A76             -71.0   130.2   164.6   160.9     ---     ---     ---       138.5(anti)   176.1(C2'-endo) ~C2'-endo      ---     ---     ---
******************************************************************************************
Virtual eta/theta torsion angles:

  eta:    C4'(i-1)-P(i)-C4'(i)-P(i+1)
  theta:  P(i)-C4'(i)-P(i+1)-C4'(i+1)
    [Ref: Olson (1980): "Configurational statistics of polynucleotide chains.
          An updated virtual bond model to treat effects of base stacking."
          Macromolecules, 13(3):721-728]

  eta':   C1'(i-1)-P(i)-C1'(i)-P(i+1)
  theta': P(i)-C1'(i)-P(i+1)-C1'(i+1)
    [Ref: Keating et al. (2011): "A new way to see RNA." Quarterly Reviews
          of Biophysics, 44(4):433-466]

  eta":   base(i-1)-P(i)-base(i)-P(i+1)
  theta": P(i)-base(i)-P(i+1)-base(i+1)

          nt                eta   theta     eta'  theta'    eta"  theta"
 1     G A.G1                ---  -139.3     ---  -136.5     ---  -110.8
 2     C A.C2              171.9  -144.6  -175.5  -144.1  -136.1  -118.1
 3     G A.G3              160.2  -151.4   173.9  -153.9  -145.0  -143.7
 4     G A.G4              164.3  -144.6   177.7  -144.1  -154.8   -98.7
 5     A A.A5              166.9  -138.1  -178.3  -135.8  -116.3  -111.6
 6     U A.U6              172.1  -149.7  -170.8  -143.9  -130.1  -126.5
 7     U A.U7             -158.0   -42.7  -138.7   -60.7  -120.5   -31.5
 8     U A.U8              162.7   160.7  -159.9  -163.8  -142.6   176.2
 9     A A.A9             -140.6   -38.9  -159.3  -112.7   157.1  -105.5
 10    g A.2MG10            27.8  -130.3    97.2  -130.1   134.8  -110.3
 11    C A.C11             170.3  -135.8  -175.7  -136.7  -137.8  -119.9
 12    U A.U12             159.9  -121.6   176.5  -130.6  -148.5  -101.4
 13    C A.C13             178.1  -179.1  -166.8   176.7  -118.5   178.4
 14    A A.A14             171.9  -146.5   172.1  -133.4  -179.7   -74.6
 15    G A.G15             164.3  -177.9  -166.6  -161.0   -92.6  -101.8
 16    u A.H2U16          -124.1   -77.5  -114.2  -108.3   -72.5  -127.0
 17    u A.H2U17           -10.5   -64.3     7.7   -94.7    17.3  -125.4
 18    G A.G18             -21.0  -167.4    45.3  -160.9    61.3  -124.2
 19    G A.G19            -127.4   -43.3  -122.0   -72.9  -105.8    -7.8
 20    G A.G20             165.3  -100.4  -160.4  -101.1  -177.9  -115.4
 21    A A.A21             -78.3   152.7   -68.0   155.1   -61.1   154.8
 22    G A.G22             159.5   167.6   156.6   178.8   157.1  -162.6
 23    A A.A23             178.4  -141.8  -173.5  -141.2  -156.1  -112.0
 24    G A.G24             163.7  -139.5   177.7  -137.6  -137.6  -103.8
 25    C A.C25             161.4  -132.6   179.2  -131.0  -128.2   -89.0
 26    g A.M2G26           173.0  -133.0  -167.7  -130.4  -106.9   -93.6
 27    C A.C27             163.5  -142.3  -178.0  -141.5  -123.6  -105.6
 28    C A.C28             157.5  -143.8   171.1  -144.3  -136.3  -125.5
 29    A A.A29             163.5  -152.9   179.0  -150.8  -142.9  -124.7
 30    G A.G30             178.3  -127.8  -167.7  -126.5  -128.2   -72.5
 31    A A.A31             165.4  -133.9  -174.3  -131.0  -101.0   -93.9
 32    c A.OMC32           164.5  -139.2  -175.9  -138.0  -122.3  -108.9
 33    U A.U33             165.1  -114.0   177.8  -158.5  -141.1   138.3
 34    g A.OMG34            27.3  -121.7    50.5  -123.7    22.7   -84.4
 35    A A.A35             162.5  -127.7  -177.7  -128.5  -116.8  -113.4
 36    A A.A36             164.9  -172.7  -174.4  -169.2  -142.3  -115.1
 37    g A.YYG37           163.1  -135.2   174.1  -131.3  -119.8   -79.8
 38    A A.A38             170.2  -133.9  -173.3  -129.0  -104.3  -105.5
 39    P A.PSU39           174.0  -132.6  -168.6  -131.2  -127.5   -89.6
 40    c A.5MC40           163.1  -148.5  -177.6  -149.3  -115.9  -131.7
 41    U A.U41             169.4  -148.8   177.2  -144.0  -152.9  -120.5
 42    G A.G42             171.2  -150.4  -171.5  -151.6  -133.9  -124.5
 43    G A.G43             174.2  -151.6  -174.4  -150.0  -134.0  -124.5
 44    A A.A44             173.2  -120.4  -171.8  -120.0  -133.3   -72.6
 45    G A.G45             168.6  -141.6  -168.3  -128.4  -103.4  -133.4
 46    g A.7MG46          -143.2  -107.3  -133.6  -149.6  -148.2  -162.7
 47    U A.U47             -31.5   -56.8     4.8   -91.0    24.9  -110.7
 48    C A.C48             -82.5    53.9   -29.3    17.5     1.5  -107.6
 49    c A.5MC49           -56.7  -145.3   -36.6  -142.8   103.2  -130.2
 50    U A.U50             174.8  -146.6  -176.9  -142.8  -153.6  -113.8
 51    G A.G51             170.3  -147.3  -175.5  -148.2  -134.2  -122.1
 52    U A.U52             160.3  -145.8   173.9  -144.3  -141.8  -119.6
 53    G A.G53             174.9  -141.5  -167.2  -142.4  -124.7  -111.6
 54    t A.5MU54           171.1  -129.2  -177.4  -122.6  -133.3   -76.4
 55    P A.PSU55           165.3  -115.2  -173.6  -155.4  -112.1   145.1
 56    C A.C56              31.4  -126.9    51.6  -124.1    25.3   -87.4
 57    G A.G57             164.3  -142.5  -174.1  -131.9  -119.2  -113.8
 58    a A.1MA58          -131.5  -108.7  -105.3  -171.2  -104.2   159.8
 59    U A.U59               1.8  -119.4    26.8  -109.9    49.0   -56.9
 60    C A.C60            -171.8   -40.7  -130.1   -68.5   -70.2   -35.8
 61    C A.C61             122.4  -148.3   168.6  -144.1  -158.2  -117.4
 62    A A.A62             173.0  -146.6  -176.9  -144.9  -142.0  -119.6
 63    C A.C63             164.5  -148.3   177.9  -149.6  -143.9  -128.6
 64    A A.A64             158.4  -151.0   168.5  -148.2  -154.8  -122.8
 65    G A.G65             173.6  -147.3  -172.0  -145.4  -130.5  -121.2
 66    A A.A66             177.6  -145.4  -170.1  -142.7  -133.5  -111.9
 67    A A.A67             165.6  -149.3  -176.9  -149.8  -129.8  -126.7
 68    U A.U68             168.9  -138.2   179.4  -136.1  -143.2   -96.5
 69    U A.U69             165.6  -160.5  -176.0  -161.2  -118.8  -156.9
 70    C A.C70             166.7  -146.2   173.6  -149.0  -171.6  -127.0
 71    G A.G71             161.0  -143.0   174.0  -142.3  -146.3  -113.4
 72    C A.C72             166.1  -141.5  -177.5  -141.9  -131.5  -110.2
 73    A A.A73             167.6  -137.8  -177.2  -133.3  -127.1   -89.8
 74    C A.C74             171.2  -122.1  -172.8  -116.5  -116.2   -72.1
 75    C A.C75             174.9   106.5  -161.9   109.8  -102.9  -139.3
 76    A A.A76               ---     ---     ---     ---     ---     ---
******************************************************************************************
Sugar conformational parameters:

  v0: C4'-O4'-C1'-C2'
  v1: O4'-C1'-C2'-C3'
  v2: C1'-C2'-C3'-C4'
  v3: C2'-C3'-C4'-O4'
  v4: C3'-C4'-O4'-C1'

  tm: the amplitude of pucker
  P:  the phase angle of pseudorotation
    [Ref: Altona & Sundaralingam (1972): "Conformational analysis
          of the sugar ring in nucleosides and nucleotides. A new
          description using the concept of pseudorotation."
          J Am Chem Soc, 94(23):8205-8212]

          nt                 v0      v1      v2      v3      v4      tm      P   Puckering
 1     G A.G1                1.7   -23.4    35.1   -35.2    21.1    36.5    16.1  C3'-endo
 2     C A.C2                1.6   -23.2    34.8   -34.8    20.9    36.2    16.1  C3'-endo
 3     G A.G3                2.7   -25.1    36.8   -36.1    21.2    38.1    14.6  C3'-endo
 4     G A.G4               -1.6   -22.3    36.3   -38.2    25.0    38.8    20.8  C3'-endo
 5     A A.A5               10.1   -32.6    41.5   -36.6    16.7    41.7     4.8  C3'-endo
 6     U A.U6                0.3   -24.0    37.3   -38.1    23.9    39.2    18.2  C3'-endo
 7     U A.U7              -24.4    35.4   -32.4    18.9     3.3    35.4   156.1  C2'-endo
 8     U A.U8                5.8   -28.7    39.7   -37.2    19.7    40.4    10.5  C3'-endo
 9     A A.A9              -31.7    41.8   -35.6    18.1     8.4    41.2   149.8  C2'-endo
 10    g A.2MG10             7.8   -28.0    36.7   -33.0    15.9    37.0     6.6  C3'-endo
 11    C A.C11               1.2   -21.2    32.1   -32.5    19.8    33.5    16.8  C3'-endo
 12    U A.U12              -4.6   -19.3    34.5   -37.9    26.7    38.1    25.2  C3'-endo
 13    C A.C13              -3.4   -19.4    33.8   -36.4    25.1    36.9    23.7  C3'-endo
 14    A A.A14              12.6   -30.8    36.8   -30.2    11.0    36.8   358.9   C2'-exo
 15    G A.G15               1.9   -24.6    36.8   -36.8    22.2    38.3    16.0  C3'-endo
 16    u A.H2U16             0.0   -18.7    29.2   -30.2    19.2    30.9    18.8  C3'-endo
 17    u A.H2U17            23.0   -36.7    35.1   -23.2     0.2    37.0   341.4   C2'-exo
 18    G A.G18             -27.9    39.5   -35.0    20.2     4.8    38.9   154.3  C2'-endo
 19    G A.G19             -17.6    31.0   -31.9    23.1    -3.8    32.7   167.6  C2'-endo
 20    G A.G20               6.6   -27.8    36.6   -34.2    17.5    37.0     8.7  C3'-endo
 21    A A.A21               3.8   -25.0    35.1   -34.4    19.4    36.0    13.0  C3'-endo
 22    G A.G22              16.4   -34.1    38.1   -29.5     8.3    38.3   353.8   C2'-exo
 23    A A.A23               4.2   -26.6    37.4   -36.5    20.1    38.3    12.6  C3'-endo
 24    G A.G24               3.9   -28.4    40.3   -39.3    22.4    41.5    13.4  C3'-endo
 25    C A.C25               0.6   -24.5    37.8   -38.0    23.6    39.6    17.4  C3'-endo
 26    g A.M2G26             6.3   -27.5    37.1   -34.7    17.9    37.6     9.3  C3'-endo
 27    C A.C27               0.2   -23.5    36.5   -37.2    23.6    38.4    18.3  C3'-endo
 28    C A.C28               6.6   -29.0    39.1   -36.3    18.8    39.6     9.2  C3'-endo
 29    A A.A29               3.4   -26.6    38.4   -37.4    21.4    39.5    13.7  C3'-endo
 30    G A.G30               2.6   -24.2    35.7   -34.9    20.4    36.9    14.5  C3'-endo
 31    A A.A31               2.6   -24.0    35.0   -34.6    20.2    36.2    14.6  C3'-endo
 32    c A.OMC32            -1.2   -21.7    35.1   -36.7    23.9    37.4    20.4  C3'-endo
 33    U A.U33               3.5   -25.4    36.5   -35.3    20.1    37.5    13.3  C3'-endo
 34    g A.OMG34             3.9   -22.7    32.2   -30.8    17.1    32.9    12.2  C3'-endo
 35    A A.A35              -2.0   -19.9    32.7   -34.9    23.4    35.2    21.9  C3'-endo
 36    A A.A36             -20.6    -7.3    30.6   -43.2    40.5    43.9    45.8   C4'-exo
 37    g A.YYG37             2.1   -24.1    36.0   -35.6    21.0    37.4    15.4  C3'-endo
 38    A A.A38              10.9   -30.3    37.6   -32.5    13.6    37.7     2.4  C3'-endo
 39    P A.PSU39             2.1   -25.6    38.5   -38.4    22.8    40.0    15.8  C3'-endo
 40    c A.5MC40             0.8   -22.5    34.6   -35.0    21.5    36.3    17.3  C3'-endo
 41    U A.U41               3.8   -27.7    39.9   -38.6    22.0    41.0    13.4  C3'-endo
 42    G A.G42              -1.7   -22.4    36.8   -38.6    25.4    39.4    20.9  C3'-endo
 43    G A.G43               4.3   -27.6    39.1   -37.6    21.1    40.1    12.6  C3'-endo
 44    A A.A44               1.0   -23.0    35.2   -35.4    21.6    36.8    16.9  C3'-endo
 45    G A.G45               2.1   -24.3    35.7   -35.4    21.2    37.0    15.4  C3'-endo
 46    g A.7MG46           -27.4    38.6   -34.7    19.7     4.7    38.5   154.5  C2'-endo
 47    U A.U47             -20.9    34.8   -35.1    24.3    -2.2    36.4   164.9  C2'-endo
 48    C A.C48             -25.6    38.4   -35.6    22.1     2.1    38.4   158.2  C2'-endo
 49    c A.5MC49             5.8   -28.1    38.7   -36.0    19.1    39.3    10.1  C3'-endo
 50    U A.U50               9.4   -32.2    41.0   -36.4    17.6    41.2     5.6  C3'-endo
 51    G A.G51               4.9   -27.9    38.9   -36.8    20.3    39.7    11.5  C3'-endo
 52    U A.U52               3.2   -28.5    41.4   -40.1    23.6    42.7    14.1  C3'-endo
 53    G A.G53              -1.0   -23.1    37.0   -38.3    24.9    39.4    19.8  C3'-endo
 54    t A.5MU54            -1.4   -22.2    35.9   -37.7    24.8    38.3    20.6  C3'-endo
 55    P A.PSU55             6.2   -29.9    40.9   -38.3    20.4    41.5    10.1  C3'-endo
 56    C A.C56               3.8   -25.3    35.7   -34.5    19.2    36.6    12.6  C3'-endo
 57    G A.G57               4.0   -26.7    37.9   -36.5    20.6    38.9    12.8  C3'-endo
 58    a A.1MA58           -24.3    38.4   -36.9    23.9     0.2    39.0   161.1  C2'-endo
 59    U A.U59              -4.4   -18.3    31.8   -35.7    25.4    35.3    25.8  C3'-endo
 60    C A.C60             -28.8    40.5   -36.4    21.2     4.7    40.3   154.8  C2'-endo
 61    C A.C61               2.6   -25.5    36.8   -36.6    21.5    38.1    14.8  C3'-endo
 62    A A.A62               5.9   -27.8    38.1   -35.4    18.8    38.7     9.9  C3'-endo
 63    C A.C63               5.4   -27.3    37.5   -35.5    19.1    38.1    10.7  C3'-endo
 64    A A.A64               4.1   -28.6    40.2   -38.8    22.2    41.2    12.9  C3'-endo
 65    G A.G65               1.5   -26.6    39.5   -39.9    24.3    41.2    16.5  C3'-endo
 66    A A.A66              -2.9   -21.6    36.5   -38.8    26.5    39.5    22.5  C3'-endo
 67    A A.A67               2.4   -24.9    36.5   -36.1    21.4    37.8    15.0  C3'-endo
 68    U A.U68               5.3   -28.4    39.5   -37.5    20.3    40.3    11.2  C3'-endo
 69    U A.U69               2.9   -26.3    38.3   -37.9    22.3    39.6    14.7  C3'-endo
 70    C A.C70               2.4   -25.9    38.7   -37.9    22.4    40.1    15.0  C3'-endo
 71    G A.G71               3.7   -27.4    39.2   -38.3    21.8    40.3    13.5  C3'-endo
 72    C A.C72              -0.6   -21.9    34.9   -36.2    23.1    37.0    19.5  C3'-endo
 73    A A.A73               2.4   -25.4    37.3   -36.9    21.8    38.6    15.0  C3'-endo
 74    C A.C74               4.4   -25.4    35.6   -34.0    18.6    36.4    11.8  C3'-endo
 75    C A.C75               2.3   -22.5    33.1   -33.0    19.2    34.3    15.1  C3'-endo
 76    A A.A76             -13.6    30.5   -34.8    27.7    -9.1    34.8   176.1  C2'-endo
******************************************************************************************
Assignment of sugar-phosphate backbone suites

  bin: name of the 12 bins based on [delta(i-1), delta, gamma], where
       delta(i-1) and delta can be either 3 (for C3'-endo sugar) or 2
       (for C2'-endo) and gamma can be p/t/m (for gauche+/trans/gauche-
       conformations, respectively) (2x2x3=12 combinations: 33p, 33t,
       ... 22m); 'inc' refers to incomplete cases (i.e., with missing
       torsions), and 'trig' to triages (i.e., with torsion angle
       outliers)
  cluster: 2-char suite name, for one of 53 reported clusters (46
           certain and 7 wannabes), '__' for incomplete cases, and
           '!!' for outliers
  suiteness: measure of conformer-match quality (low to high in range 0 to 1)

    [Ref: Richardson et al. (2008): "RNA backbone: consensus all-angle
          conformers and modular string nomenclature (an RNA Ontology
          Consortium contribution)." RNA, 14(3):465-481]

          nt             bin    cluster   suiteness
 1     G A.G1            inc      __       0
 2     C A.C2            33p      1a       0.935
 3     G A.G3            33p      1a       0.868
 4     G A.G4            33p      1a       0.842
 5     A A.A5            33p      1a       0.847
 6     U A.U6            33p      1a       0.664
 7     U A.U7            32p      1b       0.803
 8     U A.U8            23p      2a       0.509
 9     A A.A9            32p      1[       0.046
 10    g A.2MG10         23p      2g       0.640
 11    C A.C11           33p      1a       0.507
 12    U A.U12           33p      1a       0.898
 13    C A.C13           33t      1c       0.824
 14    A A.A14           trig     !!       0
 15    G A.G15           33p      1a       0.484
 16    u A.H2U16         trig     !!       0
 17    u A.H2U17         33t      !!       0
 18    G A.G18           32p      5p       0.026
 19    G A.G19           22p      4b       0.512
 20    G A.G20           23p      2a       0.623
 21    A A.A21           33t      !!       0
 22    G A.G22           33t      1f       0.714
 23    A A.A23           33p      1a       0.840
 24    G A.G24           33p      1a       0.881
 25    C A.C25           33p      1a       0.967
 26    g A.M2G26         33p      1a       0.819
 27    C A.C27           33p      1a       0.698
 28    C A.C28           33p      1a       0.923
 29    A A.A29           33p      1a       0.973
 30    G A.G30           33p      1a       0.838
 31    A A.A31           33p      1a       0.914
 32    c A.OMC32         33p      1a       0.782
 33    U A.U33           33p      1a       0.897
 34    g A.OMG34         33p      1g       0.784
 35    A A.A35           33p      1a       0.517
 36    A A.A36           33p      1a       0.670
 37    g A.YYG37         33p      1a       0.625
 38    A A.A38           33p      1a       0.903
 39    P A.PSU39         33p      1a       0.680
 40    c A.5MC40         33p      1a       0.942
 41    U A.U41           33p      1a       0.945
 42    G A.G42           33p      1a       0.630
 43    G A.G43           33p      1a       0.882
 44    A A.A44           33p      1a       0.837
 45    G A.G45           33p      1a       0.749
 46    g A.7MG46         32p      1[       0.849
 47    U A.U47           22p      4p       0.589
 48    C A.C48           22t      2u       0.283
 49    c A.5MC49         23p      6d       0.520
 50    U A.U50           33p      1a       0.656
 51    G A.G51           33p      1a       0.981
 52    U A.U52           33p      1a       0.945
 53    G A.G53           33p      1a       0.896
 54    t A.5MU54         33p      1a       0.720
 55    P A.PSU55         33p      1a       0.586
 56    C A.C56           33p      1g       0.894
 57    G A.G57           33p      1a       0.837
 58    a A.1MA58         32p      1[       0.332
 59    U A.U59           23p      4d       0.411
 60    C A.C60           32p      1b       0.662
 61    C A.C61           23p      2a       0.553
 62    A A.A62           33p      1a       0.895
 63    C A.C63           33p      1a       0.964
 64    A A.A64           33p      1a       0.791
 65    G A.G65           33p      1a       0.586
 66    A A.A66           33p      1a       0.940
 67    A A.A67           33p      1a       0.941
 68    U A.U68           33p      1a       0.891
 69    U A.U69           33p      1a       0.951
 70    C A.C70           33p      1a       0.809
 71    G A.G71           33p      1a       0.761
 72    C A.C72           33p      1a       0.832
 73    A A.A73           33p      1a       0.965
 74    C A.C74           33p      1a       0.886
 75    C A.C75           33p      1a       0.639
 76    A A.A76           32t      !!       0

Concatenated suite string per chain. To avoid confusion of lower case
modified nucleotide name (e.g., 'a') with suite cluster (e.g., '1a'),
use --suite-delimiter to add delimiters (matched '()' by default).

1   A RNA nts=76  G1aC1aG1aG1aA1aU1bU2aU1[A2gg1aC1aU1cC!!A1aG!!u!!u5pG4bG2aG!!A1fG1aA1aG1aC1ag1aC1aC1aA1aG1aA1ac1aU1gg1aA1aA1ag1aA1aP1ac1aU1aG1aG1aA1aG1[g4pU2uC6dc1aU1aG1aU1aG1at1aP1gC1aG1[a4dU1bC2aC1aA1aC1aA1aG1aA1aA1aU1aU1aC1aG1aC1aA1aC1aC!!A

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DSSR-enabled innovative PyMOL schematics in the covers of the RNA Journal

The DSSR-PyMOL schematics have been featured in all 12 cover images (January to December) of the RNA Journal in 2021. Moreover, the January 2022 issue of RNA continues to highlight DSSR-enabled schematics (see the note below). In the current Covid-19 pandemic, this cover seems to be a fit for the upcoming Christmas holiday season.

Ebola virus matrix protein octameric ring (PDB id: 7K5L; Landeras-Bueno S, Wasserman H, Oliveira G, VanAernum ZL, Busch F, Salie ZL, Wysocki VH, Andersen K, Saphire EO. 2021. Cellular mRNA triggers structural transformation of Ebola virus matrix protein VP40 to its essential regulatory form. Cell Rep 35: 108986). The Ebola virus matrix protein (VP40) forms distinct structures linked to distinct functions in the virus life cycle. VP40 forms an octameric ring-shaped (D4 symmetry) assembly upon binding of RNA and is associated with transcriptional control. RNA backbone is displayed as a red ribbon; block bases use NDB colors: A—red, G—green, U—cyan; protein is displayed as a gold ribbon. Cover image provided by the Nucleic Acid Database (ndbserver.rutgers.edu). Image generated using DSSR and PyMOL (Lu XJ. 2020. Nucleic Acids Res 48: e74).

Thanks to Dr. Cathy Lawson at the NDB for generating these cover images using DSSR and PyMOL for the RNA Journal. I’m gratified that the 2020 NAR paper is explicitly acknowledged: it’s the first time I’ve published as a single author in my scientific career.

Did you know that you can easily generate similar DSSR-PyMOL schematics via the http://skmatic.x3dna.org/ website? It is “simple and effective”, “good for teaching”, and has been highly recommended by Dr. Quentin Vicens (CU Denver) in FacultyOpinions.com.


The 12 PDB structures illustrated in the 2021 covers are:

  1. January 2021 “iMango-III fluorescent aptamer (PDB id: 6PQ7; Trachman III RJ, Stagno JR, Conrad C, Jones CP, Fischer P, Meents A, Wang YX, Ferre-D’Amare AR. 2019. Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser. Acta Cryst F 75: 547). Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold).”
  2. February 2021 “Human adenosine deaminase (E488Q mutant) acting on dsRNA (PDB id: 6VFF; Thuy-Boun AS, Thomas JM, Grajo HL, Palumbo CM, Park S, Nguyen LT, Fisher AJ, Beal PA. 2020. Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition. Nucleic Acids Res. https://doi.org/10.1093/nar/gkaa532). Adenosine deaminase enzymes convert adenosine to inosine in duplex RNA, a modification that strongly affects RNA structure and function in multiple ways.”
  3. March 2021 “Hepatitis A virus IRES domain V in complex with Fab (PDB id: 6MWN; Koirala D, Shao Y, Koldobskaya Y, Fuller JR, Watkins AM, Shelke SA, Pilipenko EV, Das R, Rice PA, Piccirilli JA. 2019. A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites. Nat Commun 10: 3629).”
  4. April 2021 “Mouse endonuclease V in complex with 23mer RNA (PDB id: 6OZO; Wu J, Samara NL, Kuraoka I, Yang W. 2019. Evolution of inosine-specific endonuclease V from bacterial DNase to eukaryotic RNase. Mol Cell 76: 44). Endonuclease V cleaves the second phosphodiester bond 3′ to a deaminated adenosine (inosine). Although highly conserved, EndoV change substrate preference from DNA in bacteria to RNA in eukaryotes.”
  5. May 2021 “Manganese riboswitch from Xanthmonas oryzae (PDB id: 6N2V; Suddala KC, Price IR, Dandpat SS, Janeček M, Kührová P, Šponer J, Banáš P, Ke A, Walter NG. 2019. Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch. Nat Commun 10: 4304). Bacterial manganese riboswitches control the expression of Mn2+ homeostasis genes. Using FRET, it was shown that an extended 4-way-junction samples transient docked states in the presence of Mg2+ but can only dock stably upon addition of submillimolar Mn2+.”
  6. June 2021 “Sulfolobus islandicus Csx1 RNase in complex with cyclic RNA activator (PDB id: 6R9R; Molina R, Stella S, Feng M, Sofos N, Jauniskis V, Pozdnyakova I, Lopez-Mendez B, She Q, Montoya G. 2019. Structure of Csx1-cOA4 complex reveals the basis of RNA decay in Type III-B CRISPR-Cas. Nat Commun 10: 4302). CRISPR-Cas multisubunit complexes cleave ssRNA and ssDNA, promoting the generation of cyclic oligoadenylate (cOA), which activates associated CRISPR-Cas RNases. The Csx1 RNase dimer is shown with cyclic (A4) RNA bound.”
  7. July 2021 “M. tuberculosis ileS T-box riboswitch in complex with tRNA (PDB id: 6UFG; Battaglia RA, Grigg JC, Ke A. 2019. Structural basis for tRNA decoding and aminoacylation sensing by T-box riboregulators. Nat Struct Mol Biol 26: 1106). T-box riboregulators are a class of cis-regulatory RNAs that govern the bacterial response to amino acid starvation by binding, decoding, and reading the aminoacylation status of specific transfer RNAs.”
  8. August 2021 “CAG repeats recognized by cyclic mismatch binding ligand (PDB id: 6QIV; Mukherjee S, Blaszczyk L, Rypniewski W, Falschlunger C, Micura R, Murata A, Dohno C, Nakatan K, Kiliszek A. 2019. Structural insights into synthetic ligands targeting A–A pairs in disease-related CAG RNA repeats. Nucleic Acids Res 47:10906). 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.”
  9. September 2021 “Corn aptamer complex with fluorophore Thioflavin T (PDB id: 6E81; Sjekloca L, Ferre-D’Amare AR. 2019. Binding between G quadruplexes at the homodimer interface of the Corn RNA aptamer strongly activates Thioflavin T fluorescence. Cell Chem Biol 26: 1159). 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.”
  10. October 2021 “Cas9 nuclease-sgRNA complex with anti-CRISPR protein inhibitor (PDB id: 6JE9; Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, et al. 2019. Structures of Neisseria meningitidis Cas9 complexes in catalytically poised and anti-CRISPR-inhibited states. Mol Cell 76: 938­–952.e5). Nme1Cas9, a compact nuclease for in vivo genome editing. AcrIIC3 is an anti-CRISPR protein inhibitor.”
  11. November 2021 “Two-quartet RNA parallel G-quadruplex complexed with porphyrin (PDB id: 6JJI; Zhang Y, Omari KE, Duman R, Liu S, Haider S, Wagner A, Parkinson GN, Wei D. 2020. Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths. Nucleic Acids Res 48: 9886–9898).”
  12. December 2021 “Structure of S. pombe Lsm1–7 with RNA, polyuridine with 3’ guanosine (PDB id: 6PPV; Montemayor EJ, Virta JM, Hayes SM, Nomura Y, Brow DA, Butcher SE. 2020. Molecular basis for the distinct cellular functions of the Lsm1–7 and Lsm2–8 complexes. RNA 26: 1400–1413). Eukaryotes possess eight highly conserved Lsm (like Sm) proteins that assemble into circular, heteroheptameric complexes, bind RNA, and direct a diverse range of biological processes. Among the many essential functions of Lsm proteins, the cytoplasmic Lsm1–7 complex initiates mRNA decay, while the nuclear Lsm2–8 complex acts as a chaperone for U6 spliceosomal RNA.”

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BioExcel webinar on DSSR

On December 9, 2021, at 15:00 CET, I will present a BioExcel webinar titled “X3DNA-DSSR, a resource for structural bioinformatics of nucleic acids.”



For the record, the screenshot of the announcement is shown below:

BioExcel webinar on DSSR

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A video overview of DSSR

Today, I released a video overview of DSSR (http://docs.x3dna.org/dssr-overview/).

DSSR has a sizable user base. However, in my opinion, DSSR is still underutilized for what it has to offer. This overview video is intended not only to attract new DSSR users, but also to highlight features that even experienced users may overlook.

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The DSSR-Jmol and DSSR-PyMOL integrations

As documented in the Overview PDF, DSSR can be easily incorporated into other structural bioinformatics pipelines. Working with Robert Hanson and Thomas Holder respectively, I initiated the integrations of DSSR into Jmol and PyMOL, two of the most popular molecular viewers. The DSSR-Jmol and DSSR-PyMOL integrations lead to unparalleled search capabilities and innovative visualization styles of 3D nucleic acid structures. They also exemplify the critical roles that a domain-specific analysis engine may play in general-purpose molecular visualization tools.

On January 27, 2016, I wrote the blogpost Integrating DSSR into Jmol and PyMOL. Four years later, these integrations have led to two peer-reviewed articles, both published in Nucleic Acids Research (NAR). This blogpost (dated 2020-09-15) highlights key features in each case and reflects on my experience in these two exciting collaborations.

The DSSR-Jmol integration

Hanson RM and Lu XJ (2017). DSSR-enhanced visualization of nucleic acid structures in Jmol. The DSSR-Jmol integration excels in its SQL-like, flexible searching capability of structural features, as demonstrated at the website http://jmol.x3dna.org. This work fills a gap in RNA structural bioinformatics by enabling deep analyses and SQL-like queries of RNA structural characteristics, interactively. Here are some simple examples:

SELECT WITHIN(dssr, "nts WHERE is_modified = true") # modified nucleotides
SELECT pairs # all pairs
Select WITHIN(dssr, "pairs WHERE name = 'Hoogsteen'") # Hoogsteen pairs
SELECT WITHIN(dssr, "pairs WHERE name != 'WC'") # non-Watson-Crick pairs
SELECT junctions # all junctions loops
select within(dssr, "junctions WHERE num_stems = 4") # four-way junction loops

In a recently email communication, Bob wrote:

How are you doing? I’m smiling, because I am remembering our incredible, animated discussions and how fun it was to work together with you on Jmol and DSSR.

The DSSR-PyMOL integration

Lu XJ (2020). DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL. The DSSR-PyMOL integration brings unprecedented visual clarity to 3D nucleic acid structures, especially for G-quadruplexes. The four interfaces cover virtually all conceivable use cases. The easiest way to get started and quickly benefit from this work is via the web application at http://skmatic.x3dna.org.

I approached Thomas to write the DSSR-PyMOL manuscript together, in a similar way as the DSSR-Jmol paper. He wrote back, saying “I’m not interesting in being co-author of the paper”, adding:

But, if there is anything I can help you with, like revising the `dssr_block.py` script, or proof-reading the PyMOL related parts of the manuscript, I’ll be happy to do so.

Indeed, Thomas helped in several aspects of the DSSR-PyMOL project, as acknowledged in the paper:

I appreciate Thomas Holder (PyMOL Principal Developer, Schrödinger, Inc.) for writing the DSSR plugin for PyMOL, and for providing insightful comments on the manuscript and the web application interface.

Enhanced vs Innovative

Some viewers may noticed the difference in titles of the two NAR papers: “DSSR-enhanced visualization of nucleic acid structures in Jmol” vs. “DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL”. As a matter of fact, the initial title of the DSSR-PyMOL paper was DSSR-enhanced visualization of nucleic acid structures in PyMOL, as shown in the December 02, 2019 announcement post on the 3DNA Forum.

In an era where reproducibility of “scientific” publications has become an issue and “break-throughs” are often broken or hardly held, I hesitate to use phrases such as “innovative”, “novel”, “paradigm shift” etc. Instead, I often use the modest words “refinement”, “enhance”, “improved”, “revised” etc, and try to deliver more than claimed. However, reviewers may take solid work but modest writing as “incremental” or “unexciting”. Before submitting the DSSR-PyMOL paper, I changed the title to DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL. Does it mean that the DSSR-PyMOL integration is more innovative than the DSSR-Jmol case? Not necessarily. I do have a paper with “innovative” in its title.

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