Question: Is there a way to translate amino acid sequences into atomic sequences?
0
gravatar for Naresh
3.0 years ago by
Naresh60
Korea, Republic Of
Naresh60 wrote:

Hi, Is there any software which will translate amino acid sequence into atomic sequences.

Please help me.

Kind regards Naresh

sequence • 1.2k views
ADD COMMENTlink modified 3.0 years ago by Ibrahim Tanyalcin930 • written 3.0 years ago by Naresh60
3

What are "Atomic sequences"?

ADD REPLYlink written 3.0 years ago by genomax65k

I mean to say at atomic level., such as C,N,O,S,H.

ADD REPLYlink written 3.0 years ago by Naresh60

So you want to convert MCNSSC (peptide) into C230 N30 H200 O23 S34 (this example is non-sense but something like adding up all C's, N's, S', O' etc)?

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by genomax65k

https://www.google.co.kr/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=CARd%3A+Carbon+distribution+analysis+program+for+protein+sequences

Please see this paper. He has made an algorithm for changing protein sequence to atomic levels..

ADD REPLYlink written 3.0 years ago by Naresh60
2
gravatar for wdiwdi
3.0 years ago by
wdiwdi380
Germany
wdiwdi380 wrote:

Yes. Newer (3.454 and later) versions of the Cactvs Cheminformatics toolkit (academic downloads at www.xemistry.com/academic) support the decoding of 1- and 3-letter amino acid codes into atomic connection tables (with stereochemistry).

Example command line, Python version (you'd probably script it instead of typing it), which writes two sample mini peptides as SD files:

cspy
pycactvs>e=Ens('aa:AlaGluAsn')
pycactvs>Molfile.Write('minipeptide1.sdf',e)
[ens0]
pycactvs>e=Ens('aa:AEN')
pycactvs>Molfile.Write('minipeptide2.sdf',e)
[ens1]
pycactvs>
ADD COMMENTlink written 3.0 years ago by wdiwdi380

Read protein sequence MCNSSCMGGMNRR Change into atomic sequence CCCCCSNOHHHHHHHHHCCCSNOHHHHHHHHCCCCNNOOHHHHHHCCCNOOOHHHHHHHCCCC

ADD REPLYlink written 3.0 years ago by Naresh60
1

Why not write a simple script? Pretty much all you need is amino acid to atoms translation table.

ADD REPLYlink modified 3.0 years ago • written 3.0 years ago by 5heikki8.4k

This is confusing. What is the meaning of this?

ADD REPLYlink written 3.0 years ago by wdiwdi380

If you take the protein sequence - M stands for Methionine. at the atomic level, Methionine is made of atoms like C,N,O,S,H.. So, my need is that if i give protein sequence, the software must change into atomic level like C,N,O,S,H.

Hope you understand my question now..

ADD REPLYlink written 3.0 years ago by Naresh60
1

I think we understand what your question is, I don't think anybody understands why.

ADD REPLYlink written 3.0 years ago by Emily_Ensembl18k

Here is an answer for the "why": C: Is there a way to translate amino acid sequences into atomic sequences?

ADD REPLYlink written 3.0 years ago by genomax65k
eseq=''
t=Table.Ref('elementdata')
for a in 'MCNSSCMGGMNRR':
        with Ens('aa:'+a) as e:
                e.hadd()
                for i,count in enumerate(e.E_ELEMENT_COUNT):
                        eseq += t.cellget(i,'symbol')*count
print(eseq)

Output: HHHHHHHHHHHCCCCCNOOSHHHHHHHCCCNOOSHHHHHHHHCCCCNNOOOHHHHHHHCCCNOOOHHHHHHHCCCNOOOHHHHHHHCCCNOOSHHHHHHHHHHHCCCCCNOOSHHHHHCCNOOHHHHHCCNOOHHHHHHHHHHHCCCCCNOOSHHHHHHHHCCCCNNOOOHHHHHHHHHHHHHHCCCCCCNNNNOOHHHHHHHHHHHHHHCCCCCCNNNNOO

If you have any element order sorting criteria - this is left as an exercise to the reader (judging from your sample desired output, you are not using the standard Hill system)

ADD REPLYlink written 3.0 years ago by wdiwdi380
1
gravatar for Ibrahim Tanyalcin
3.0 years ago by
Belgium
Ibrahim Tanyalcin930 wrote:

Dear,

Try opening a pdb file with a text editor :).

Regards,

ADD COMMENTlink written 3.0 years ago by Ibrahim Tanyalcin930
0
gravatar for Keith Callenberg
3.0 years ago by
Pittsburgh, PA
Keith Callenberg890 wrote:

Do you really want just an atomic sequence? Or are you asking for the molecular structure in 2D or 3D?

In either case, you should keep in mind that back-translation (amino acid sequence to nucleotide sequence) will be ambiguous given that multiple codons code for each amino acid. You can use a tool like Backtranseq to convert from amino acid sequence to nucleotide sequence and it will use the most common codons for a given organism: http://www.ebi.ac.uk/Tools/st/emboss_backtranseq/

If you do want the molecular structure, you can then give the nucleotide sequence to a free, open-source tool like 3DNA: http://x3dna.org/

There is also a web-based version if you just want to test it out: http://w3dna.rutgers.edu/rebuild. Just select a DNA type and enter the sequence.

Both the offline and online versions will generate a PDB that can be looked at either in a text editor, or visualized with software like VMD or PyMOL. The w3dna online version also offers an in-browser viewer called Jmol for visualization.

ADD COMMENTlink modified 3.0 years ago • written 3.0 years ago by Keith Callenberg890
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