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.
The current version of DSSR is v2.4.5-2024sep24 which contains miscellaneous bug fixes (e.g., chain id with > 4 chars) and minor improvements. This release synchronizes with the new R24 funding, which will bring the project to the next level. All existing users are encouraged to upgrade their installation.
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all features described in the three DSSR-related papers, and includes the originally separate SNAP program (still unpublished) for analyzing DNA/RNA-protein complexes.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.
By default, DSSR produces RNA secondary structures in three commonly used file formats––ViennaRNA package dbn, Mfold connect table (.ct), and CRW bpseq––that can be fed directly into visualization tools such as VARNA. In this blog post, I want to dig deeper into the bpseq format, and show the variations available from DSSR.
According to "RNA STRAND v2.0 - The RNA secondary STRucture and statistical ANalysis Database" (with slight editing):
BPSEQ format:The file name should end with the suffix ".bpseq", as in "mystr.bpseq". The bpseq format is a simple text format in which there is one line per base in the molecule, listing the position of the base (leftmost position is 1), the base name (A,C,G,U, or other alphabetical characters), and the position number of the base to which it is paired, with a 0 denoting that the base is unpaired. For more information, see the Comparative RNA Web Site. An example is as follows:
1 G 8
2 G 7
3 C 0
4 A 0
5 U 0
6 U 0
7 C 2
8 C 1
For complexes with more than one molecule, the molecules are listed in sequence, with the base pairs numbers of each successive molecule following in order from the previous molecule.
The bases in bpseq format are identified by position numbers starting from 1 for the leftmost position. That is the convention DSSR follows by default in its .bpseq output. For example, for the PDB entry 1msy, which contains 27 nucleotides, the command x3dna-dssr -i=1msy.pdb will generate a file named dssr-2ndstrs.bpseq with the following contents (abbreviated):
1 U 0
2 G 26
3 C 25
......
25 G 3
26 U 2
27 G 0
However, according to PDB atomic coordinates, the nucleotides are numbered from U2647 (#1) to G2673 (#27) as shown in the Figure 1 below:
--
Figure 1. 3D and 2D structures of PDB entry 1msy. (A) 3D schematic auto-created via the DSSR-PyMOL integration. The labeled residues follow PDB coordinates. (B) 2D diagram rendered with VARNA using DSSR-derived 2D structural information in the .ct format. This figure was annotated using Inkscape.
It makes sense that the labelling of bases in the 2D bpseq format follows those from the 3D atomic coordinates in the PDB. Thus instead of starting from position 1 as shown above, the bpseq file would start with 2647. That's exactly what the DSSR --bpseq option is created for. Thus, with the command x3dna-dssr -i=1msy.pdb --bpseq, the output file dssr-2ndstrs.bpseq now has the following contents (abbreviated):
2647 U 0
2648 G 2672
2649 C 2671
......
2671 G 2649
2672 U 2648
2673 G 0
This .bpseq file can be read by VARNA (tested with VARNAv3-93.jar) to generate a 2D image as shown in Figure 1(B) above.
Moreover, with the command x3dna-dssr -i=1msy.pdb --bpseq=extra, the output file dssr-2ndstrs.bpseq now contains additional info to easily identify a nucleotide and its pairing partener:
2647 U 0 # name=A.U2647
2648 G 2672 # name=A.G2648, pairedNt=A.U2672
2649 C 2671 # name=A.C2649, pairedNt=A.G2671
......
2671 G 2649 # name=A.G2671, pairedNt=A.C2649
2672 U 2648 # name=A.U2672, pairedNt=A.G2648
2673 G 0 # name=A.G2673
It should be noted that this .bpseq output file is no longer compliant to the standard, and can not be fed into VARNA for visualization.
The --bpseq option has been added upon users' request. The --bpseq=extra variation was implemented recently to ensure that the --bpseq option by itself produce a valid .bpseq file without extra info (e.g., enabled with the global --more option). Now the extra info for .bpseq output is enabled only by setting --bpseq=extra explicitly.
This --bpseq option and its evolution is a good example of how DSSR responds to community requests. I'm here to listen and I'm always willing to improve DSSR that better fit users' needs. If you make use of DSSR in your pipeline and need some adaptions, please do not hesitate to contact me. I may consider adding a new option or revising the code otherwise that would streamline the integration of DSSR into your project.
DSSR commands used, and the output .bpseq files:
x3dna-dssr -i=1msy.pdb
cp dssr-2ndstrs.bpseq 1msy-dssr-default.bpseq
x3dna-dssr -i=1msy.pdb --bpseq
cp dssr-2ndstrs.bpseq 1msy-dssr-bpseq.bpseq
x3dna-dssr -i=1msy.pdb --bpseq=extra
cp dssr-2ndstrs.bpseq 1msy-dssr-bpseq-extra.bpseq
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
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:
- 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).”
- 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.”
- 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).”
- 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.”
- 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+.”
- 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.”
- 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.”
- 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.”
- 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.”
- 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.”
- 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).”
- 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.”
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:
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.
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.
Recently, while reading the Miskiewicz et al. review article How bioinformatics resources work with G4 RNAs, I noticed the term DSSR-G4DB under the category Databases with G4-related data. It refers to the website http://G4.x3dna.org (or g4.x3dna.org) that has been there since 2017 and weekly updated with new G-quadruplexes from the PDB. The DSSR-G4 resource, DSSR-Enabled Automatic Identification and Annotation of G-quadruplexes in the PDB, has already been cited several times in literature. However, I have not written up a paper on it yet, and thus have never thought carefully on a name for the resource. The term DSSR-G4DB sounds good to me, and I may well use it in the future.
Given below are the relevant quotations on DSSR and the DSSR-G4DB resource in the Miskiewicz et al. review article and my notes. The underlined headings (e.g., “Conclusion”) are those of the Miskiewicz et al. review article.
Methods: Databases with G4-related data
Currently, there exist 16 databases, which store information concerning quadruplexes. They fall into three categories: databases that collect primary or tertiary structures with experimentally verified G4s (DSSR-G4DB, G4IPDB, G4LDB, G4RNA, Lit392 and Lit638); databases storing data from high-throughput sequencing with mapped quadruplexes (GSE63874, GSE77282, GSE110582 and GSE129281); and databases of sequences with G4s identified in silico (Greglist, GRSDB2, G4-virus, Non-B DB v2.0, Plant-GQ and QuadBase2)
DSSR-G4DB [38] contains quadruplex nucleic acid structures found by DSSR in the Protein Data Bank [30], currently 354 entries. The data are annotated. Users can find information about G-tetrads, G4 helices and G4-stems and visualize the 3D models of G4 structures. Availability: webserver (http://g4.x3 dna.org). Recent update: 5 June 2020.
Note: DSSR-G4DB is updated weekly. The latest update is on 2020-09-09, with 362 G-quadruplexes auto-curated with DSSR from the PDB.
Methods: Tools that analyze and visualize 2D and 3D structure
Currently, four tools can analyze and visualize G4 structures. DSSR [38] … ElTetrado [31] … RNApdbee [66, 69] … 3D-NuS [65]
DSSR [38] processes the 3D structure of the RNA molecule and annotates its secondary structure. It is a part of the 3DNA suite [67] designed to work with the structures of nucleic acids. DSSR identifies, classifies and describes base pairs, multiplets and characteristic motifs of the secondary structure; helices, stems, hairpin loops, bulges, internal loops, junctions and others. It can also detect modules and tertiary structure patterns, includ- ing pseudoknots and kink-turns. The recent extension, DSSR- PyMOL [68], allows drawing cartoon-block schemes of the 3D structure and responds to the need for simplified visualization of quadruplexes. Input data formats: PDB, mmCIF and PDB ID. Availability: standalone program, web application (http://dssr.x3 dna.org/, http://skmatic.x3dna.org/).
Note: The other three tools all depend on or make use of DSSR and 3DNA:
- ElTetrado “ElTetrado depends on DSSR (Lu, Bussemaker and Olson, 2015) in terms of detection of base pairing and stacking.”
- RNApdbee uses 3DNA/DSSR as the default to identify base pairs.
- 3D-NuS employs 3DNA for structural analysis and model building.
“These filtrated structures (225 DNA and 166 RNA structures) have been used to derive the local base pair step and base pair parameters (Table S2 for DNA and Table S3 for RNA) using 3DNA software package [35] and are stored in the server for 3D-NuS modeling.”
“Soon after the user submits input for sequence-specific modeling, the server fetches the appropriate base pair step and base pair parameters from the database and creates a 3DNA style input file. Subsequently, the template model is built using the rebuild module of 3DNA software package and subjected to energy optimization using X-plor [56] to remove steric hindrance, specifically in the mismatch- containing duplexes (Fig. 1).”
Results: Computational experiments with structure-based tools
DSSR and ElTetrado identified quadruplexes in the input PDB files. Both programs focused on structural aspects of the input molecule, explicitly informing about quadruplexes and tetrads within the structure. DSSR provided an extensive analysis of 3D structures and output the data about G-tetrads, G-helices and G4-stems. It computed planarity for each G-tetrad and gave the sections area, rise and twist parameters for G4-helix and G4-stems. The program automatically assigned loop topologies according to the predefined types (P—parallel, D—diagonal and L—lateral) and their orientation (+/−). DSSR-PyMOL generated block schemes of both quadruplexes (Figure 4A3 and B3). ElTetrado also calculated planarity, rise and twist parameters and identified strand directions for both quadruplexes. It classified the quadruplexes and their component tetrads to ONZ classes. Finally, it generated the arc diagram (Figure 4A1 and B1) and two-line dot-bracket encoding of every quadruplex.
Note: DSSR contains an undocumented option --G4. With the ONZ variant, i.e., --g4=onz (case does not matter), DSSR also outputs the ONZ classification of G-tetrads from the same chain.
Conclusion
DSSR comprehensively examines the G4 structure, determines a variety of its parameters and provides the schematic 3D view.
It is worth noting that DSSR has been categorized under “Databases with G4-related data” and “Tools that analyze and visualize 2D and 3D structure” of the Methods section. It is not a tool that predicts G4 location in the sequence. There are 14 tools listed in “Table 2. Selected features of PQS prediction tools”, including G4Hunter and QGRS Mapper etc.
Recently, while visiting the NAR website on DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL, I noticed a big red circle ① near “View Metrics”. I was quite curious to see what it meant. After a few clicks, I was delighted to read the following recommendation in Faculty Opinions by Quentin Vicens:
I really enjoyed “playing” with the revised and expanded version of Dissecting the Spatial Structure of RNA (DSSR) described by Xiang-Jun Lu in this July issue of NAR. The software is known to generate ‘block view’ representations of nucleic acids that make many parameters more immediately visible, such as base composition, stacking, and groove depth. This new version includes Watson-Crick pairs shown as single rectangles, and G quadruplexes as large squares, making such regions more quickly distinguishable from other regions within an overall tertiary structure. I was amazed at how simple and effective the web interface was, and I liked the possibility to download a PyMOL session to look at molecules under different angles. If need be, blocks can be further edited in PyMOL using the provided plugin (see on page 35). I highly recommend it!
The DSSR-PyMOL schematics paper/website has been rated “Very Good”, and classified as “Good for Teaching”. See Vicens Q: Faculty Opinions Recommendation of [Lu XJ, Nucleic Acids Res 2020 48(13):e74]. In Faculty Opinions, 14 Aug 2020; 10.3410/f.738001682.793577327.
DSSR 2.0 is out. It integrates an unprecedented set of features into one computational tool, including analysis/annotation, schematic visualization, and model building of 3D nucleic acid structures. DSSR 2.0 supersedes 3DNA 2.4, which is still maintained but no additional features other than bug fixes are scheduled. See the DSSR 2.0 overview PDF.
DSSR delivers a great user experience by solving problems and saving time. Considering its usability, interoperability, features, and support, DSSR easily stands out among `competitors’. It exemplifies a `solid software product’. I strive to make DSSR a pragmatic tool that the structural bioinformatics community can count on.
DSSR 2.0 is licensed by Columbia University. The software remains free for academic users, with the basic user manual. The professional user manual (over 230 pages, including 7 appendices) is available for paid academic users or commercial users only. Licensing revenue helps ensure the long-term sustainability of the DSSR project.
Additionally, the paper “DSSR-enabled innovative schematics of 3D nucleic acid structures with PyMOL” has recently been published in Nucleic Acids Research, 48(13):e74. Check the web interface.
The DSSR-PyMOL paper/website has been rated “very good” and classified as “Good for Teaching”. See Vicens Q: Faculty Opinions Recommendation of [Lu XJ, Nucleic Acids Res 2020 48(13):e74]. In Faculty Opinions, 14 Aug 2020; 10.3410/f.738001682.793577327
