Is there a way to translate amino acid sequences into atomic sequences?

Question

[Naresh]

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

Please help me.

Kind regards Naresh

[GenoMax]

What are "Atomic sequences"?

[Naresh]

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

[GenoMax]

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)?

[Naresh]

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..

Answer 1

[wdiwdi]

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>

[Naresh]

Read protein sequence MCNSSCMGGMNRR Change into atomic sequence CCCCCSNOHHHHHHHHHCCCSNOHHHHHHHHCCCCNNOOHHHHHHCCCNOOOHHHHHHHCCCC

[5heikki]

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

[wdiwdi]

This is confusing. What is the meaning of this?

[Naresh]

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..

[Emily]

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

[GenoMax]

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

[wdiwdi]

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)

Answer 2

[Ibrahim Tanyalcin]

Dear,

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

Regards,

Answer 3

[Keith Callenberg]

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.