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Messages - lvelve0901

Pages: [1] 2 3 4
1
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

2
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




3
RNA structures (DSSR) / Re: Bulge motif
« on: November 13, 2017, 11:07:40 am »
I understand.

Thanks.

Best,
Honglue

4
RNA structures (DSSR) / Re: Definition of Helix Form
« on: November 13, 2017, 11:06:08 am »
I actually did some work to benchmark whether 3DNA did a good job to identify the helix form.

In our lab, we have an in-hosue database of all the DNA stem and RNA stem structures from the entire crystal structures labeled "Protein#DNA" and "Protein#RNA" deposited in RCSB with resolution under 4Å. Yes, I use DSSR to generate stem structures for each PDB.

Then I build fiber idealized B form DNA and idealized A form RNA using 3DNA. If you type

fiber -m

It will generate a list of different nucleic acid model, I pick the number 4 for B-DNA and number 20 for A-RNA.

[hs189@summer:Plot] fiber -m
Fiber data in directory: /home/hs189/X3DNA/fiber/

id#  Twist   Rise        Structure description
   (degree) (Angstrom)
-------------------------------------------------------------------------------
 1   32.7   2.548  A-DNA  (calf thymus; generic sequence: A, C, G and T)
 2   65.5   5.095  A-DNA  poly d(ABr5U) : poly d(ABr5U)
 3    0.0  28.030  A-DNA  (calf thymus) poly d(A1T2C3G4G5A6A7T8G9G10T11) :
                                        poly d(A1C2C3A4T5T6C7C8G9A10T11)
 4   36.0   3.375  B-DNA  (calf thymus; generic sequence: A, C, G and T)
 5   72.0   6.720  B-DNA  poly d(CG) : poly d(CG)
 6  180.0  16.864  B-DNA  (calf thymus) poly d(C1C2C3C4C5) : poly d(G6G7G8G9G10)
 7   38.6   3.310  C-DNA  (calf thymus; generic sequence: A, C, G and T)
 8   40.0   3.312  C-DNA  poly d(GGT) : poly d(ACC)
 9  120.0   9.937  C-DNA  poly d(G1G2T3) : poly d(A4C5C6)
10   80.0   6.467  C-DNA  poly d(AG) : poly d(CT)
11   80.0   6.467  C-DNA  poly d(A1G2) : poly d(C3T4)
12   45.0   3.013  D-DNA  poly d(AAT) : poly d(ATT)
13   90.0   6.125  D-DNA  poly d(CI) : poly d(CI)
14  -90.0  18.500  D-DNA  poly d(A1T2A3T4A5T6) : poly d(A1T2A3T4A5T6)
15  -60.0   7.250  Z-DNA  poly d(GC) : poly d(GC)
16  -51.4   7.571  Z-DNA  poly d(As4T) : poly d(As4T)
17    0.0  10.200  L-DNA  (calf thymus) poly d(GC) : poly d(GC)
18   36.0   3.230  B'-DNA alpha poly d(A) : poly d(T) (H-DNA)
19   36.0   3.233  B'-DNA beta2 poly d(A) : poly d(T) (H-DNA  beta)
20   32.7   2.812  A-RNA  poly (A) : poly (U)


I know that the 3DNA identify the helix form in a dinucleotide step so I generated two base pair long idealized B-DNA and A-RNA to align the coordinate of the stem structures I generated using only backbone and sugar heavy atom and yielded an alignment RMSD for each dinucleotide step in my database.

Here is the result:

My RMSD cutoff is 2Å.

Protein#DNA
Total number of entries (dinucleotide step): 97366
Number of entries with RMSD (> 2Å) but 3DNA think it is B form: 49
Number of entries with RMSD (< 2Å) but 3DNA think it is X form (ambiguous): 29702
The rest of entries is 3DNA agree with my RMSD cut off.

Protein#RNA
Total number of entries (dinucleotide step): 56530
Number of entries with RMSD (> 2Å) but 3DNA think it is A form: 0
Number of entries with RMSD (< 2Å) but 3DNA think it is X form (ambiguous): 22893
The rest of entries is 3DNA agree with my RMSD cut off.

I think 3DNA basically did a good job considering the number of entries that excess the RMSD cutoff but 3DNA think it is A/B form among the entire PDB.
I am just wondering does 3DNA also simply use coordinate alignment to identify the helix form?

Best,
Honglue

PS. these data is under publication so I am not sure if I can provide further details but I will try my best to give you as much detain as you want.

5
RNA structures (DSSR) / Re: FRABASE
« on: November 13, 2017, 10:06:40 am »
I see.

Thanks.

Best,
Honglue

6
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« on: November 13, 2017, 10:05:22 am »
Hi Xiangjun,

Your answer is very clear and concrete. I think now I understand how 3DNA identify the H-bonds in general. I will keep posting other PDB examples in the future if we find something wired in the Hbond section since my rotation students is manually inspecting them now. Do you think we should post here or start a new topic in this forum for other PDB?

Also, I tried your way to parse json using jq and it works. But the issue by doing this


x3dna-dssr -i=3bnq.pdb --symm --get-hbond --json | jq .hbonds[1]


You will first run the DSSR and generate json file. Sometimes for a large PDB file it will take a long time. Is there any command to parse json if we have already generated the json file?

Thanks.

Best,
Honglue

7
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« on: November 11, 2017, 05:54:22 pm »
Hi Xiangjun,

Sorry I have been busy with other stuff in lab but I do remember your question last time.

----------------------------------------------------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------------------------------------------------------------
For your last question:


Quote
{u'index': 31, u'atom2_serNum': 212, u'residue_pair': u'nt:aa', u'distance': 3.09, u'atom_pair': u'N:N', u'atom2_id': u'N@2:B.ALA6', u'donAcc_type': u'standard', u'atom1_id': u'N3@2:A.DG3', u'atom1_serNum': 69}

How did you get the above output for PDB id: 1PFE? Specifically, where does the 'u' before each tag name come from?


Basically, I just load the json use my way (my own json parser) and print out the 'hbonds' section. In my python, when I load the json file (using import json module), the string format will be loaded as unicode. I think that's why those string will have the 'u'. I think that is just my python string encode issue. Here is more explanation of the unicode string (https://stackoverflow.com/questions/21808657/what-is-a-unicode-string). I also tried your way as you suggested (using jq) but I didn't make it work. Do I need to install jq in my computer? I installed jq from the website
https://stedolan.github.io/jq/ and put the file in my working folder then type.

x3dna-dssr -i=3bnq.pdb --symm --get-hbond --json | jq . hbonds[1]

However, it outputs

Processing file '3bnq.pdb'
jq: error: Could not open file hbonds[1]: No such file or directory


I don't know if I did the right way.

----------------------------------------------------------------------------------------------------------------------------------------------------------
----------------------------------------------------------------------------------------------------------------------------------------------------------
My new questions:

My new target structure is Mitochondrial Ribosomal Decoding Site (PDB ID: 3BNQ). I downloaded the PDB file (not biological assembly file) from RCSB. Then I try to generate the json file by typing:

x3dna-dssr -i=3bnq.pdb -o=3bnq.json --json --more --symm

I use my own json parser to look for the hydrogen bond between the RNA and the ligand PAR.

There are three examples with different don_Acc type here. All the hydrogen bonds mentioned below are labeled in the 3bnq.pse. Measure01 is the first example. Measure02 is the second example. Measure03 is the third example.

Example 1: Hbond index 117. donAcc_type acceptable.
{u'index': 117, u'atom2_serNum': 1928, u'residue_pair': u'nt:ligand', u'distance': 2.612, u'atom_pair': u'O:O', u'atom2_id': u'O41@C.PAR101', u'donAcc_type': u'acceptable', u'atom1_id': u'OP2@C.G22', u'atom1_serNum': 1426}

This is a hydrogen bond between a hydroxyl group in the ligand PAR and the OP2 atom in rG22.

Example 2: Hbond index 113. donAcc_type standard.
{u'index': 113, u'atom2_serNum': 1937, u'residue_pair': u'nt:ligand', u'distance': 2.63, u'atom_pair': u'O:N', u'atom2_id': u'N32@C.PAR101', u'donAcc_type': u'standard', u'atom1_id': u'OP2@C.C21', u'atom1_serNum': 1406}

This is a hydrogen bond between a amino group in the ligand PAR and the OP2 atom in rC21.

In both cases, it seems that the hydrogen bond geometry are very similar then why does the DSSR think they are different donAcc_type?

Example 3: Hbond index 107. donAcc_type questionable.
{u'index': 107, u'atom2_serNum': 1367, u'residue_pair': u'nt:nt', u'distance': 3.358, u'atom_pair': u'O:O', u'atom2_id': u"O4'@C.G19", u'donAcc_type': u'questionable', u'atom1_id': u"O4'@C.A17", u'atom1_serNum': 1323}

In this case, the DSSR identify a hbonds between two O4' atom, but we know that for ribose, the O4' is unlikely to be protonated. Is this the reason why DSSR think the donAcc_type is questionable?

I really appreciate your help.

Best,
Honglue



8
RNA structures (DSSR) / Re: General questions of H-bond section in DSSR
« on: November 10, 2017, 10:35:42 pm »
Hi Xiangjun,

I have follow up questions in terms of donAcc_type in H-bond.

Here I attach the json output file of PDB 3BNQ. In the H-bond section, I see there are three types of donAcc_type: standard, acceptable and questionable. You have already explained to me what questionable mean but could you please explain the difference between standard and acceptable?

Also, is there anyway to tell which atom is donor and which atom is acceptor?

Thank you.

Best,
Honglue

9
RNA structures (DSSR) / General questions of H-bond section in DSSR
« on: November 01, 2017, 11:37:03 am »
Hi Xiangjun,

Sorry I gave a long list of questions yesterday. Here, I just post a few questions in terms of the H-bond in DSSR json.

For the H-bond between protein/peptide/ligand to nucleic acid, my target structure is 1PFE, which is a DNA bound to an antibiotic, echinomycin. I downloaded the biological assembly file and used the following command:

x3dna-dssr -i=1PFE.pdb -o=1PFE.json --json --more --symm

In the "hbonds" session of the output json file, I did found the all the DNA-drug interactions. For example,

{u'index': 31, u'atom2_serNum': 212, u'residue_pair': u'nt:aa', u'distance': 3.09, u'atom_pair': u'N:N', u'atom2_id': u'N@2:B.ALA6', u'donAcc_type': u'standard', u'atom1_id': u'N3@2:A.DG3', u'atom1_serNum': 69}

However, I have a few questions in terms of the hbonds output.

(1) How do I know which atom is H-bond donor and which is acceptor, like do you always put acceptor in the first place(atom1)?
(2) If the 'donAcc_type' is questionable, what does it mean? Does it mean that DSSR probably doesn't guess the valence properly?
(3) Wha does the 'serNum' mean here?

Here, I attached all my files.

Thank you.

Best,
Honglue

10
Hi Xiangjun,

First, I want to apologize for not getting the feedback to you in time, though I carefully benchmarked the calculation as you suggested.

1. H-bond
For the H-bond between protein/peptide/ligand to nucleic acid, my target structure is 1PFE, which is a DNA bound to an antibiotic, echinomycin. I downloaded the biological assembly file and used the following command:

x3dna-dssr -i=1PFE.pdb -o=1PFE.json --json --more --symm

In the "hbonds" session of the output json file, I did found the all the DNA-drug interactions. For example,

{u'index': 31, u'atom2_serNum': 212, u'residue_pair': u'nt:aa', u'distance': 3.09, u'atom_pair': u'N:N', u'atom2_id': u'N@2:B.ALA6', u'donAcc_type': u'standard', u'atom1_id': u'N3@2:A.DG3', u'atom1_serNum': 69}

I have a few questions in terms of the hbonds output.

(1) How do I know which atom is H-bond donor and which is acceptor, like do you always put acceptor in the first place(atom1)?
(2) If the 'donAcc_type' is questionable, what does it mean? Does it mean that DSSR probably doesn't guess the valence properly?
(3) Generally speaking, for a random ligand (not peptide-linking or DNA/RNA-linking), how does DSSR guess the valence, like how to guess which heavy atom should be bonded to hydrogen?
(4) Wha does the 'serNum' mean here?

I am training a rotation student to use DSSR to parse all the drug and nucleic acid interactions from the entire PDB so hopefully we will keep updating the issues of DSSR hbonds under the same page.

--------------------------------------------------------------------------------

2. metal

I got a bit confused about your metal sessions in the json file.

My target structure is 1HR2. It is a P4P6 domain which has many Mg2+ in the coordinates.

I again downloaded the biological assembly file and tried to type:

x3dna-dssr -i=1HR2.pdb -o=1HR2.json --json --more --symm --metal

In the output json file, there is indeed a session called 'metals'. For example,

{u'index': 3, u'ligands_long': u'', u'num_ligands': 0, u'symbol': u'Mg', u'ligands_short': u'', u'id': u'A.MG55'}
{u'index': 4, u'ligands_long': u'A.A248,A.U249,A.G250', u'num_ligands': 3, u'symbol': u'Mg', u'ligands_short': u'AUG', u'id': u'A.MG57'}

In the index 3, I assume it means there is no residue/ligand interact with MG55 right? However, if you open the PDB file, don't you think that MG55 is very closed to the cytosine 255? I guess I might misunderstand something, so my questions in terms of metals are.

(1) How does DSSR define the interactions with metal involved?
(2) More generally, how doesn't DSSR define a metal. For example,

In the structure 1D8X, the COBALT HEXAMMINE(III) (NCO) which is a metal complex is considered as metal in DSSR.
In the structure 3MGV, the VANADATE ION (VO4) which is already an negative charged ion is considered as metal in DSSR.

Is there any list which DSSR think certain atom belongs to metal category?

--------------------------------------------------------------------------------

Again, I really appreciate your help with my research all the time and really hope DSSR will be better and better.

Thanks again.

Best,
Honglue

11
Gotcha, I realized that Json file actually has what I need in the 'hbonds' section.

Also, is there also a section for metal in the pdb file. For example, how many metal-RNA interaction in the PDB file?

Best,
Honglue

12

For example, in the dssr, there is a --get-hbond option. It will output all the H-bonds within two nucleotide and it gives you the distance, donor and acceptor etc., but I guess that only applies for nucleic acid. There is no way to detect H-bond between for example protein-and nucleic acid in current DSSR, right?

If not, do you have any suggestion of any software which can do something like parse the interactions between protein/peptide/ligand and nucleic acids.

Really appreciate your help.

Best,
Honglue

13
RNA structures (DSSR) / Can DSSR detect nucleic acid ligand interaction
« on: October 31, 2017, 03:48:34 pm »
Hi Xiangjun,

I am just curious whether DSSR can detect something like RNA and ligand/metal interaction in a PDB file.
For example, list all the hydrogen bond between RNA and ligand?

Best,
Honglue

14
RNA structures (DSSR) / FRABASE
« on: October 18, 2017, 11:35:30 am »
Hi Xiangjun,

Do you have any idea that how different between DSSR and some online RNA database such as FRABASE in terms of secondary structure identification.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-231

Thanks.

Best,
Honglue

15
RNA structures (DSSR) / Re: Definition of Helix Form
« on: September 15, 2017, 05:03:35 pm »
Hi Xiangjun,

Could you please tell me when you will report the detail of helix form definition in dssr? My advisor asked me some questions in terms of how dssr identify helix form so I would like to know more details of this.

This is not urgent so please take your time.

Thank you so much.

Best,
Honglue

Pages: [1] 2 3 4

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.