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Questions and answers => RNA structures (DSSR) => DSSR-NAR paper => Topic started by: xiangjun on July 04, 2015, 07:53:36 am

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Title: Summary table
Post by: xiangjun on July 04, 2015, 07:53:36 am
The only table in the paper presents a summary of common structural features identified by DSSR (in default settings) for ten representative RNA molecules. The screen-captured image of the table shown below is from a DSSR poster, where the citations to the PDB entries have been removed for simplicity.

(http://x3dna.bio.columbia.edu/dssr-nar/table-summary.png)

This table aims to illustrate the applicability of DSSR on a broad range of typical RNA molecules, from the classic yeast phenylalanine (1ehz (http://www.rcsb.org/pdb/explore/explore.do?structureId=1ehz)) and the new env22 twister ribozyme (4rge (http://www.rcsb.org/pdb/explore/explore.do?structureId=4rge)) to the whole E. coli 70S (5afi (http://www.rcsb.org/pdb/explore/explore.do?structureId= 5afi) ) and S. cerevisiae 80S (4u4o (http://www.rcsb.org/pdb/explore/explore.do?structureId=4u4o)) ribosomes. In each case, the listed results are produced by running DSSR automatically, as shown below:

Code: [Select]
x3dna-dssr -i=1ehz.pdb -o=1ehz.out
x3dna-dssr -i=4u4o.cif -o=4u4o.out
Note that either the old .pdb or the new .cif (PDBx/mmCIF) format, as downloaded directly from the PDB, can be fed into DSSR. The time it requires to finish each analysis would obviously depend on hardwire configurations. For example, one of the reviewers tested DSSR on a Windows machine, and reported "08:20 min on the unprocessed 4U4O.cif file". That's why in the 'time' column, only a rough value is presented. The point is that DSSR runs almost instantaneously on a contemporary laptop computer, except for the analyses of very large ribosomal RNA structures.

To ensure accuracy and for easy verification, the table itself was generated semi-automatically with a Ruby script, which produced a text file (named 'summary.txt') with content as follows:

Code: [Select]
|name|id|nt|pair|multiplet|helix|stem|hairpin|iloop|junction|pseudoknot|time|
|tRNA|1ehz|76(14)|34(21)|4|2|4|3|0(0)|1|1|00:00|
|tRNA mimicry|4p5j|84(1)|37(27)|4|2|5|5|0(0)|1|1|00:00|
|Twister ribozyme|4rge (chain A)|56(0)|31(20)|4|2|6|2|0(0)|1|2|00:00|
|SAM-I riboswitch|2gis|95(1)|47(30)|8|3|7|3|3(1)|2|1|00:00|
|Cas9-RNA-DNA|4oo8|117(0)|49(43)|0|5|6|4|1(1)|0|0|00:00|
|Group I intron|1gid (chain A)|158(0)|82(48)|14|4|10|3|4(4)|1|0|00:00|
|Group II intron|3bwp|349(0)|159(104)|12|10|23|6|9(1)|2|4|00:01|
|Large ribosomal subuit|1s72|2876(5)|1459(811)|242|86|179|68|67(36)|36|3|00:31|
|E. coli ribosome-EF-TU complex|5afi|4801(53)|2383(1332)|325|134|297|116|126(66)|54|2|02:45|
|Yeast 80S ribosome|4u4o|10398(0)|4927(2705)|572|317|636|231|348(139)|120|4|06:07|
Within the org-mode (http://orgmode.org) of emacs, the above text file can be automatically expanded into a neatly formated form:

Code: [Select]
| name                           | id             |       nt |       pair | multiplet | helix | stem | hairpin |    iloop | junction | pseudoknot |  time |
| tRNA                           | 1ehz           |   76(14) |     34(21) |         4 |     2 |    4 |       3 |     0(0) |        1 |          1 | 00:00 |
| tRNA mimicry                   | 4p5j           |    84(1) |     37(27) |         4 |     2 |    5 |       5 |     0(0) |        1 |          1 | 00:00 |
| Twister ribozyme               | 4rge (chain A) |    56(0) |     31(20) |         4 |     2 |    6 |       2 |     0(0) |        1 |          2 | 00:00 |
| SAM-I riboswitch               | 2gis           |    95(1) |     47(30) |         8 |     3 |    7 |       3 |     3(1) |        2 |          1 | 00:00 |
| Cas9-RNA-DNA                   | 4oo8           |   117(0) |     49(43) |         0 |     5 |    6 |       4 |     1(1) |        0 |          0 | 00:00 |
| Group I intron                 | 1gid (chain A) |   158(0) |     82(48) |        14 |     4 |   10 |       3 |     4(4) |        1 |          0 | 00:00 |
| Group II intron                | 3bwp           |   349(0) |   159(104) |        12 |    10 |   23 |       6 |     9(1) |        2 |          4 | 00:01 |
| Large ribosomal subuit         | 1s72           |  2876(5) |  1459(811) |       242 |    86 |  179 |      68 |   67(36) |       36 |          3 | 00:31 |
| E. coli ribosome-EF-TU complex | 5afi           | 4801(53) | 2383(1332) |       325 |   134 |  297 |     116 |  126(66) |       54 |          2 | 02:45 |
| Yeast 80S ribosome             | 4u4o           | 10398(0) | 4927(2705) |       572 |   317 |  636 |     231 | 348(139) |      120 |          4 | 06:07 |
Note again, the time column -- here it is based on an iMac, which is much quicker than the 2011 MacBook Air used to produce the resultant table in the paper.

Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University