conversion of DNA sequence to PDB format

Question

[ashamscsoft]

I need to convert DNA sequence to PDB format.In that conversion, I have a doubt for example if i take information from HGMD and the reference sequence, with that informations i will convert the sequence to fasta format. Now i need to convert the fasta format to PDB format. PDB format in the sense which we will download in the Protein Data Bank. I tried converting in Open babel GUI,it was converted in PDB format. But when i give that PDB format for docking in web server it says error that your PDB file is incomplete. Since it is converting in that software it has no end statement in that conversion. I do not know what to do. Is there anyother tool for conversion? or is there anyother way to convert it? Kindly help me please

[venu]

When a protein's structure is discovered through any experimental technique (Crystallography, NMR etc), it's amino acid (all atom) coordinates are deposited in PDB. So when you are trying to convert a DNA sequence to PDB format, there are multiple steps involved. First of all, you'll need to convert your nucleotide sequence to amino acid sequence. Then search for a homologus amino acid sequence with your sequence, whose structure is available in PDB. Then use that protein structure to model (Eg: Modeller) your amino acid sequence into a structure/ PDB format. If you don't find any homologus sequence, you may follow ab initio method to derive the structure.

[ashamscsoft]

I have one doubt can u clarify? For unknown protein structure that is for our target sequence, when we do homology modeling is all the six steps necessary? or template identification is enough?

And one more doubt is after template identification why we need to do sequence alignment? is that necessary? can u help please?

[Ram]

all six steps

Ummm, what six steps? Where did you get that number from?

Template identification involves sequence alignment. Where does the "after" part come from? Is there a paper/manual you're referring to, perhaps? If so, please share a link to that here.

[ashamscsoft]

ya i have seen in many pages wait i will send the link http://vlab.amrita.edu/?sub=3&brch=277&sim=1492&cnt=1. This is one link where i saw

Answer 1

[mbnobari]

>Q8YEK5
MSVNHAYAGPGIFINDGTDDGCIWTFDKEDYSPIGDYFGNTAPADKDSAGRNSPASVKYH
IPSIQQLGGAATLKCLSKDRDTQTARVLFYGNSKEQGSISLTLGGELFVNNGNLGLGGGT
DTKAMRIGSMATLTGPSGLRSLAIGAGEIATVASGDDAIAIGTAAQAAHVGSIALGLQST
TELPSLVKDVTINGIKLSAFAGSNPASVLSIGNDTLKRSITNVGAGRVSKDSTDAVNGSQ
LYAVAEQATLGWNLTVNGMDKSRVGPGDTVDLSNSDGNLVLSKKGKDVTFNLASDLKVTS
LVAGNTFLDTNGLVITGGPSMTVSGIDAGHLKISHVANGAVTATSTDAVNGRQLFAVSEQ
AASGWSLTVNGMDKSRVGPGDTVDLSNSDGNLVLSKKGKDVTFNLASDLKVTSLVAGNTF
LDTNGLVITGGPSMTVSGIDAGQLKISHVADGAVTVTSTDAVNGSQLHRVAHTIAEHLGG
DAHVNADGPSSGRNIRCRKTLQDDL

[WouterDeCoster]

And what is the aim of posting that sequence here?

Answer 2

[max.rempel2]

This a wonderful online tool for converting DNA sequence to PDB

http://milou.science.uu.nl/enmr/services/3DDART/DARTcustombuild.html

convert DNA sequence to PDB