Messages

1

RNA structures (DSSR) / Re: How to detect very distorted base pair?

« on: September 13, 2020, 12:31:45 pm »

Dear Xiangjun,

I have two more examples of very distorted base pairs in existing PDB structures that X3DNA-DSSR is not able to detect it. I would like to know the reason and whether there is anyway to adjust the cutoff to be able to detect it?

(1) PDBID: 4NCB nt1: C.DT14 nt2: D.DA6
(2) PDBID: 5LGY nt1: E.DA17 nt2: F.DT5

Thanks.

Best,
Honglue

2

RNA structures (DSSR) / Re: How to detect very distorted base pair?

« on: January 20, 2020, 07:03:32 pm »

I see what is going on!

I was using DSSR version v1.6.5-2017jan22 and it failed to detect such base pair.

By using a new version you gave me before v1.9.4-2019jul08, I am able to detect it. Thanks.

3

RNA structures (DSSR) / How to detect very distorted base pair?

« on: January 20, 2020, 05:09:25 pm »

Dear Xiangjun,

I have a structure of a very distorted G-C base pair (C is modified) see attached. I want to output the base pair parameters like shear, buckle, opening but if I detect the base pair in DSSR it is not in the pair list. Could you please let me know how to analyze such very distorted base pair? Do I need to modify any cutoff?

Thanks.

Best,
Honglue

4

DNA/RNA-protein interactions (SNAP) / About sugar-pi stacking

« on: October 17, 2019, 04:36:41 pm »

Hi Xiangjun,

Is sugar-pi stacking currently implemented in the most updated version of SNAP? I am trying analyze the TBP-DNA interaction by using SNAP (PDB: 1QNE)

In the paper: Wilson, K. A., et al. (2014). "DNA-protein pi-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar." Nucleic Acids Res 42(10): 6726-6741. (https://academic.oup.com/nar/article/42/10/6726/2435280).

The author detect four sugar-pi interaction in the supplementary table.

Amino Acid         Nucleotide
Res Chain ResID Res Chain ResID
F   A   74    A   C   209   sugar-π
F   A   165    T   D   225   sugar-π
F   A   148    A   C   204   sugar-π

When I tried to use x3dna-snap to analyze the structure by typing:
x3dna-snap -i=1qne.pdb --t-shape --more

The output seems only report nt-AA pi-pi stacking.
****************************************************************************
List of 2 base/amino-acid stacks
       id   nt-aa   nt           aa      vertical-distance   plane-angle
   1  1qne  A-phe  C.DA204      A.PHE148        3.45             18
   2  1qne  T-phe  D.DT220      A.PHE57         3.57             23

Could you please let me know whether this is what we expected? Do you know if there are other softwares that can be used to analyze the stacking interaction in general between protein and DNA?

Thank you so much.

Best,
Honglue

5

RNA structures (DSSR) / Re: strange exception

« on: July 07, 2019, 10:58:23 pm »

Hi Xiangjun,

It seems the new version (Jul8) works very well for all my trajectory for now.

By the way I am benchmarking your new version using a ribosomal structure (PDB 1FFK).

Here I attached the output using version 2017jan22 (x3dna-dssr-old) and 2019jul08 (x3dna-dssr).

Here is the output:


[hs189@summer:version] x3dna-dssr-old -i=1ffk.pdb -o=1ffk_old.json --more --json   

Processing file '1ffk.pdb'
    total number of base pairs: 1450
    total number of multiplets: 241
    total number of helices: 85
    total number of stems: 176
    total number of isolated WC/wobble pairs: 49
    total number of atom-base capping interactions: 211
    total number of splayed-apart dinucleotides: 327
    total number of hairpin loops: 66
    total number of bulges: 34
    total number of internal loops: 65
    total number of junctions: 35
-- kissing-loops in '1ffk.pdb', hairpin loops (#1/#3) have 2 interactions [#8, #9 ...]
    total number of A-minor (type I and II) motifs: 98
    total number of ribose zippers: 41
    total number of kink turns: 7
    total number of non-loop single-stranded segments: 31
    total number of kissing loops: 5

Time used: 00:00:00:50




[hs189@summer:version] x3dna-dssr -i=1ffk.pdb -o=1ffk.json --more --json

Processing file '1ffk.pdb'
    total number of nucleotides: 2828
    total number of amino acids: 3656
    total number of base pairs: 1428
    total number of multiplets: 238
    total number of helices: 83
    total number of stems: 175
    total number of isolated WC/wobble pairs: 50
    total number of atom-base capping interactions: 211
    total number of splayed-apart dinucleotides: 400
                        consolidated into units: 251
    total number of hairpin loops: 66
    total number of bulges: 37
    total number of internal loops: 65
    total number of junctions: 35
    total number of non-loop single-stranded segments: 29
-- kissing-loops in '1ffk.pdb', hairpin loops (#1/#3) have 2 interactions [#8, #9 ...]
    total number of kissing loops: 5
    total number of A-minor (types I and II) motifs: 99
    total number of eXtended A-minor (type X) motifs: 55
    total number of ribose zippers: 41
    total number of kink turns: 8

Time used: 00:00:01:17



For example, it seems the new version detect less base pairs, less multiplets, is that because you adjust the criteria for base pair or something?

If you think this post should be in a separate topic, could you please help move it to a proper place?

Best,
Honglue

6

RNA structures (DSSR) / Re: strange exception

« on: July 05, 2019, 03:56:00 pm »

OK, I will restart using the version today.

7

RNA structures (DSSR) / Re: strange exception

« on: July 05, 2019, 03:15:59 pm »

Hi Xiangjun,

So do you update a new version today? I am still running the version you upload yesterday on my trajectory. It seems that it took longer than I expected.

Best,
Honglue

8

RNA structures (DSSR) / Re: strange exception

« on: July 04, 2019, 10:18:12 am »

Awesome. I am rerunning the new DSSR on my trajectory now and hopefully I will give you feedback this afternoon.

Happy 4th of July!

9

RNA structures (DSSR) / Re: strange exception

« on: July 03, 2019, 12:32:21 pm »

Hi Xiangjun,

By the way, I always keep using a very old version of DSSR which is v1.6.5-2017jan22. Now that since I am probably going to switch to this new version, could you please remind me of locations of the update log including all the details of modification? I couldn't find it in the website.

If you could briefly highlights some important changes I would even more appreciate.

Thank you.

Best,
Honglue

10

RNA structures (DSSR) / Re: strange exception

« on: July 03, 2019, 11:36:50 am »

Hi Xiangjun,

Interesting, these trajectories were generated by Rosetta FARFAR which I believe utilizing a library from existing PDB. However, it seems it somehow generate some new conformational space that DSSR cannot recognize it, right?

Thank you so much for your help as always.

Best,
Honglue

11

RNA structures (DSSR) / Re: strange exception

« on: July 02, 2019, 11:10:38 pm »

Command: x3dna-dssr -i=S_000331_021.pdb
Date and time: Tue Jul  2 23:22:26 2019
File name: S_000331_021.pdb
    no. of DNA/RNA chains: 1 [_=25]
    no. of nucleotides:    25
    no. of atoms:          796
    no. of waters:         0
    no. of metals:         0
    total number of base pairs: 9
    total number of multiplets: 1
    total number of helices: 1
    total number of stems: 1
    total number of isolated WC/wobble pairs: 3
    total number of atom-base capping interactions: 1
    total number of hairpin loops: 1
Uncaught exception 'Assertion failed' raised at [fncs_loop.c:1657]
aborting...

Time used: 00:00:00:01

12

RNA structures (DSSR) / Re: strange exception

« on: July 02, 2019, 11:09:56 pm »

Hi Xiangjun,

There are three pdb files in my trajectory that the new version DSSR (Jul4) cannot parse, it basically pops up the exact same error.

Best,
Honglue

13

RNA structures (DSSR) / Re: strange exception

« on: July 02, 2019, 01:11:09 pm »

Gotcha. I am testing the new version on all of my trajectory now. I should be able to give you some update by end of today.

14

RNA structures (DSSR) / Re: strange exception

« on: July 02, 2019, 01:06:31 pm »

Yes, I downloaded in this way. It is just it said the version is still may25 above that confuses me.

15

RNA structures (DSSR) / Re: strange exception

« on: July 02, 2019, 01:01:11 pm »

Is it here?

16

RNA structures (DSSR) / Re: strange exception

« on: July 02, 2019, 12:55:16 pm »

The new version will be released on July 4th right?

17

RNA structures (DSSR) / Re: strange exception

« on: July 01, 2019, 07:56:11 pm »

Hi Xiangjun,

It does work for this PDB structure. I am testing whether it works for the rest of my trajectory.

Best,
Honglue

18

RNA structures (DSSR) / strange exception

« on: June 30, 2019, 08:48:31 pm »

Hi Xiangjun,

I was trying to use DSSR to parse this attached PDB file.

x3dna-dssr -i=S_000300_115.pdb

However, the program complain an error:

Command: x3dna-dssr -i=S_000300_115.pdb
Date and time: Sun Jun 30 20:57:27 2019
File name: S_000300_115.pdb
    no. of DNA/RNA chains: 1 [_=25]
    no. of nucleotides:    25
    no. of atoms:          796
    no. of waters:         0
    no. of metals:         0
    total number of base pairs: 11
    total number of multiplets: 1
    total number of helices: 2
    total number of stems: 1
    total number of isolated WC/wobble pairs: 3
    total number of atom-base capping interactions: 1
    total number of splayed-apart dinucleotides: 3
    total number of hairpin loops: 1
Uncaught exception 'Assertion failed' raised at [fncs_loop.c:1564]
aborting...

Do you know what is going on?

Thanks.

Best,
Honglue

19

DNA/RNA-protein interactions (SNAP) / Re: Implement Json

« on: March 13, 2018, 02:30:50 pm »

Hi Xiangjun,

Thank you so much for your reply.

(1) Format:

I am thinking the similar format for DSSR should work great. If I remember it correctly, in DSSR json, you have an object called "hbonds" which you store all the hbonds pair right? For example:

[yuze@summer:dssr_learn] jq .hbonds[1] 6tna.json       
{
  "index": 2,
  "atom1_serNum": 20,
  "atom2_serNum": 1564,
  "donAcc_type": "standard",
  "distance": 2.663,
  "atom1_id": "N1@1:A.G1",
  "atom2_id": "N3@1:A.C72",
  "atom_pair": "N:N",
  "residue_pair": "nt:nt"
}

I think similar structure is fine. You can also add stacking interaction as a separate object in the json file.

By the way, in the introduction, you said

SNAP recognizes and outputs base-amino-acid H-bonding and stacking interactions.

Does that mean SNAP cannot output nucleic acid backbone interaction (only nucleic acid base)?

(2) Feedback:

I am currently training an undergraduate to analyze the interaction mode of RNA and protein. We will do the analyze for all the deposited protein RNA structures in RCSB. So we will definitely provide useful feedback when we encounter some wired cases.

Best,
Honglue

20

DNA/RNA-protein interactions (SNAP) / Re: Implement Json

« on: March 10, 2018, 09:56:30 pm »

I am trying to benchmark the staking interaction between nucleic acid base and amino acid side chain using SNAP. I think it will be easier for me to parse the information with json.

Best,
Honglue

21

DNA/RNA-protein interactions (SNAP) / Re: Implement Json

« on: March 10, 2018, 09:45:52 pm »

Awesome.

Could you please let me know when you finish it?

Best,
Honglue

22

DNA/RNA-protein interactions (SNAP) / Implement Json

« on: March 10, 2018, 09:43:32 pm »

Hi Xiangjun,

Do you plan to implement Json output for SNAP?

Best,
Honglue

23

RNA structures (DSSR) / Re: Can DSSR detect stacking interaction between ligand and nucleic acid

« on: November 16, 2017, 11:25:12 pm »

Hi Xiangjun,

Also, generally speaking, can DSSR detect protein/peptide and nucleic acid stacking interaction? For example, the stacking between aromatic ring of Phenylalanine and nucleic acid base?

Best,
Honglue

24

RNA structures (DSSR) / Can DSSR detect stacking interaction between ligand and nucleic acid

« on: November 16, 2017, 11:22:19 pm »

Hi Xiangjun,

My new target structure is 1F1T from RCSB. It is a malachite green aptamer with a ligand called N,N'-TETRAMETHYL-ROSAMINE (ROS).
If you go to the PDB website and search for this PDB, you can see there is a stacking interaction between ROS and one of the adenine base in the 2D Diagram & Interactions.

http://www.rcsb.org/pdb/explore/explore.do?structureId=1f1t

My question is whether DSSR can detect such ligand and RNA interaction?

Here, I also attach the PDB file and json file that I generated for your convenience.

Best,
Honglue

25

RNA structures (DSSR) / Re: Bulge motif

« on: November 13, 2017, 11:07:40 am »

I understand.

Thanks.

Best,
Honglue