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Questions and answers => RNA structures (DSSR) => Topic started by: lvelve0901 on April 26, 2017, 12:50:57 pm

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Title: How to look for abasic site using DSSR
Post by: lvelve0901 on April 26, 2017, 12:50:57 pm
Hi Xiangjun,

Long time no contact. I hope you had a good time recently.

I have a question about DSSR. Can DSSR detect abasic site?

For example, in 1l2c.pdb and 1l2d.pdb, there is a abasic site HPD18DG7. I thought this could be written in internal loop; however, the internal loop only detect a lower base pair open (DA23DT2).

Best,
Honglue
Title: Re: How to look for abasic site using DSSR
Post by: xiangjun on April 26, 2017, 01:56:41 pm
Hi Honglue,

As shown in Fig.1 (see below) of the DSSR paper (https://academic.oup.com/nar/article/43/21/e142/2468098/DSSR-an-integrated-software-tool-for-dissecting), "Nucleotides are recognized using standard atom names and base planarity." Since abasic sites (e.g., HPD18 in chain C of PDB id 1l2c (http://www.rcsb.org/pdb/explore/explore.do?structureId=1l2c)) do not have proper base atoms, they are not recognized as nucleotides by DSSR to begin with. Naturally, they do not appear in later analysis results of DSSR output. This is just the way DSSR works and you may take it as a deficiency. Please let me know if you have a better way to handle such cases.

(https://oup.silverchair-cdn.com/oup/backfile/Content_public/Journal/nar/43/21/10.1093_nar_gkv716/2/m_gkv716fig1.png?Expires=1493322620&Signature=YRFIrvGafWFuglGsiHTXKgGBKRJ8bbwyYQH-UYMZFvfVL27tX0PsNWUnVQIGDUNXNdxC2QtAm38snSphBoCpYFezPvh9Ujg8e4r1YwYRuaxGdi9Eg3rJYVkzqFiK~~t3Hb0LkS-ajT6BlDdWykC0FraM0bKnJND~jXHp0dxrI85sm2od4zEs7782DxdHhHA-n7Pzb7p8rYb5dwD7Czhyge3cTdfz5Sjt88u0iiNlwIEFR1YAZqwMnvsOM3-4xUmhIyC8O2tfSFD0K1YwJKw4EGh4e-G4OAkz2u~NFhpbO7p8O5PzSTchPoBADustVsi0RC8WApIlDpJlszAuWD9bsg__&Key-Pair-Id=APKAIUCZBIA4LVPAVW3Q)

Hope this clarifies your confusions.

Xiang-Jun
Title: Re: How to look for abasic site using DSSR
Post by: lvelve0901 on April 26, 2017, 03:23:57 pm
Does that mean DSSR cannot detect abasic site, since there is no base atom?

Thanks.

Best,
Honglue
Title: Re: How to look for abasic site using DSSR
Post by: xiangjun on May 01, 2017, 11:35:39 pm
Hi Honglue,

I've added an option --abasic to DSSR to take abasic sites as nucleotides, as long as main-chain backbone atoms are preserved: P, O5', C5', C4', C3', and O3'. Quick tests on 1l2c (http://www.rcsb.org/pdb/explore/explore.do?structureId=1l2c) and 1l2d (http://www.rcsb.org/pdb/explore/explore.do?structureId=1l2d) show that this new DSSR feature is working as designed (e.g., C.HPD18 is listed in an internal loop). Understandably, the abasic nucleotides won't be involved in base pairing and stacking interactions.

The DSSR on the download page (still labeled v1.6.8-2017mar28) has been updated. Have a try and report back if it solves your problem.

Xiang-Jun
Title: Re: How to look for abasic site using DSSR
Post by: kazi956 on November 27, 2023, 09:58:01 am
Quote from: xiangjun on May 01, 2017, 11:35:39 pm
Hi Honglue,

I've added an option --abasic to DSSR to take abasic sites as nucleotides, as long as main-chain backbone atoms are preserved: P, O5', C5', C4', C3', and O3'. Quick tests on 1l2c (http://www.rcsb.org/pdb/explore/explore.do?structureId=1l2c) and 1l2d (http://www.rcsb.org/pdb/explore/explore.do?structureId=1l2d) show that this new DSSR feature is working as designed (e.g., C.HPD18 is listed in an internal loop). Understandably, the abasic nucleotides won't be involved in base pairing and stacking interactions.

The DSSR on the download page (still labeled v1.6.8-2017mar28) has been updated. Have a try and report back if it solves your problem.

Xiang-Jun

Hi, I am trying to use --abasic command (./x3dna-dssr --abasic -i=test.pdb) on version 1.9.8(2019Oct16), but it's not recognizing the abasic site even if I have P, O5', C5', C4', and C3' atoms. Wondering if --abasic works properly only on the DSSR v1.7.2-2017nov20 release; if so, how can I download the older version? Thank you! 
Title: Re: How to look for abasic site using DSSR
Post by: xiangjun on November 27, 2023, 10:14:42 am
Quote
2.  Be specific with your questions; provide a minimal, reproducible
        example if possible; use attachments where appropriate.

Title: Re: How to look for abasic site using DSSR
Post by: kazi956 on November 27, 2023, 11:26:41 am
Hello, for instance, in PDB 1FZL, there is an abasic site, and the residue is a modified nucleotide with the resname PYP (pyrene deoxyriboside). X3DNA is not recognizing that residue. However, I see that for residue 3DR (on chain B), where only the sugar-phosphate backbone is present, x3dna is recognizing that and computing backbone torsions. Is there any way to compute backbone torsions for non-standard residues like PYP? Thank you!
Title: Re: How to look for abasic site using DSSR
Post by: xiangjun on November 27, 2023, 11:54:06 am
For PDB entry: 1FZL


x3dna-dssr -v

Code: [Select]
******************************************************************
           DSSR: an Integrated Software Tool for
          Dissecting the Spatial Structure of RNA
           v2.4.2-2023may01 by xiangjun@x3dna.org
******************************************************************

x3dna-dssr -i=1FZL.pdb

Code: [Select]
   1  C ( A.DC1   0.012  anti,~C2'-endo,BI,non-stack,canonical,helix-end,stem-end,coaxial-stack
   2  A ( A.DA2   0.020  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
   3  C ( A.DC3   0.007  anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack
   4  A ( A.DA4   0.018  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
   5  A ( A.DA5   0.015  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
   6  A ( A.DA6   0.015  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem,coaxial-stack
   7  C ( A.DC7   0.009  anti,~C2'-endo,canonical,non-pair-contact,helix,stem,coaxial-stack
   8  A ( A.DA8   0.013  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop
   9  ? . A.PYP9  ---    modified,~C2'-endo,BI,non-stack,internal-loop
  10  G ( A.DG10  0.013  anti,~C2'-endo,BI,canonical,non-pair-contact,helix,stem-end,coaxial-stack,internal-loop

more dssr-torsions.txt
Code: [Select]
          nt               alpha    beta   gamma   delta  epsilon   zeta     e-z        chi            phase-angle   sugar-type    ssZp     Dp    splay
 1     C A.DC1               ---     ---    59.6   143.0  -178.2   -98.9    -79(BI)   -112.1(anti)   162.0(C2'-endo) ~C2'-endo     1.99    2.26   16.42
 2     A A.DA2             -92.0  -166.3    54.8   121.4   179.5   -87.3    -93(BI)   -112.9(anti)   143.5(C1'-exo)  ~C2'-endo     1.97    2.07   18.44
 3     C A.DC3             -62.7   166.0    58.6   144.3  -166.0  -165.5     -1(--)    -85.4(anti)   156.7(C2'-endo) ~C2'-endo     2.70    2.79   25.63
 4     A A.DA4             -75.7  -177.0    60.4   153.3  -175.3   -78.8    -97(BI)   -110.7(anti)   185.3(C3'-exo)  ~C2'-endo     1.72    1.82   18.57
 5     A A.DA5             -80.9   172.3    59.3   107.1  -166.5   -94.1    -72(BI)   -126.1(anti)   120.9(C1'-exo)  ~C2'-endo     2.48    2.58   18.91
 6     A A.DA6             -74.4   171.8    59.7   120.9   179.8   -99.1    -81(BI)   -120.3(anti)   134.2(C1'-exo)  ~C2'-endo     2.37    2.43   16.58
 7     C A.DC7             -74.1  -176.0    59.0   149.2  -164.1  -146.5    -18(--)    -93.5(anti)   168.5(C2'-endo) ~C2'-endo     2.04    2.06   24.91
 8     A A.DA8             -74.9   176.5    57.1   147.6  -173.6  -100.2    -73(BI)   -120.0(anti)   175.2(C2'-endo) ~C2'-endo      ---     ---     ---
 9     ? A.PYP9            -63.0   175.7    62.6   135.3  -178.2   -77.7   -101(BI)      ---         151.8(C2'-endo) ~C2'-endo      ---     ---     ---
 10    G A.DG10            -84.6   171.5    59.9   122.1  -176.2  -130.1    -46(BI)   -112.0(anti)   133.5(C1'-exo)  ~C2'-endo     2.63    2.71   21.35

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