How to convert protein sequence into PDB format?

[TiongSY]

I'm dealing with CesA protein which there is no full 3D structure in PDB database yet. How to do the my full protein structure prediction?
I always get less than 10% of the predicted structure only from a few Protein prediction server or programme.

Your opinion and sharing are greatly appreciated!

[Juan Pedro Luna-Arias]

Have you try the iTASSER web server? It is able to perform modeling ab initio.

 

Dr. Juan Pedro Luna-Arias
Departamento de Biología Celular
Cinvestav-IPN
Av. IPN 2508 Col. Zacatenco
07360 México D.F.
Tel 52-55-57473800 ext 5512 y 5567

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From: TiongSY <tsyi...@gmail.com>
To: predictprot...@googlegroups.com
Sent: Wednesday, July 25, 2012 12:05 AM
Subject: [predictprotein-science:637] How to convert protein sequence into PDB format?

I'm dealing with CesA protein which there is no full 3D structure in PDB database yet. How to do the my full protein structure prediction?
I always get less than 10% of the predicted structure only from a few Protein prediction server or programme.

Your opinion and sharing are greatly appreciated!

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[Ravi Pratap Barnwal]

did you try I-tasser?

http://zhanglab.ccmb.med.umich.edu/I-TASSER/

regards
ravi

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[Rajesh Kumar Kesharwani]

please read this article.

http://www.google.co.in/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&sqi=2&ved=0CFUQFjAA&url=http%3A%2F%2Fwww.pelagiaresearchlibrary.com%2Fadvances-in-applied-science%2Fvol1-iss1%2FAASR-2010-1-1-158-165.pdf&ei=4r0QUM71Cc7HrQe63IHwCw&usg=AFQjCNHF9aJc0frFYiFNU8tdLhr8AlM_jw&sig2=T0h3DY1WFTr0fCz4eoTOUg

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Thanks & Regards
Rajesh Kumar Kesharwani
Division of Applied Science and Indo-Russian Center For Biotechnology [IRCB],
Indian Institute of Information Technology
Deoghat, Jhalwa
Allahabad (U.P.)
Pin: 211012
Phone: +91-900551008





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[Alessandro Maiorana]

You can try to use I-TASSER and/or ROBETTA for predicting the 3d structure.

2012/7/25 TiongSY <tsyi...@gmail.com>

I'm dealing with CesA protein which there is no full 3D structure in PDB database yet. How to do the my full protein structure prediction?
I always get less than 10% of the predicted structure only from a few Protein prediction server or programme.

Your opinion and sharing are greatly appreciated!

--

[dr.Khaled saad]

How big is that amino acid sequence? Have u used swiss prot pdb generator yet? The entry file size is important because usually gets split into seperate pdb fIles that can't be connected into 1 pdb that gives a final 3D model unless manually.

Awaiting reply..

Sent using BlackBerry® from mobinil

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From: TiongSY <tsyi...@gmail.com>

Sender: predictprot...@googlegroups.com

Date: Tue, 24 Jul 2012 22:05:56 -0700 (PDT)

To: <predictprot...@googlegroups.com>

ReplyTo: predictprot...@googlegroups.com

Subject: [predictprotein-science:637] How to convert protein sequence into PDB format?

I'm dealing with CesA protein which there is no full 3D structure in PDB database yet. How to do the my full protein structure prediction?
I always get less than 10% of the predicted structure only from a few Protein prediction server or programme.

Your opinion and sharing are greatly appreciated!

[Juan Pedro Luna-Arias]

Here you are:

http://zhanglab.ccmb.med.umich.edu/I-TASSER/

They say ab initio analysis can be done.

Good luck

JP
 

Dr. Juan Pedro Luna-Arias
Departamento de Biología Celular
Cinvestav-IPN
Av. IPN 2508 Col. Zacatenco
07360 México D.F.
Tel 52-55-57473800 ext 5512 y 5567

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From: Juan Pedro Luna-Arias <juanp...@yahoo.com>
To: "predictprot...@googlegroups.com" <predictprot...@googlegroups.com>
Sent: Wednesday, July 25, 2012 8:11 PM
Subject: Re: [predictprotein-science:638] How to convert protein sequence into PDB format?

[Avijit Patra]

in this case you go through I-Tasser server 

--

AVIJIT PATRA

Senior Research Fellow

Molecular biology & Microbiology

Department of Aquatic Animal Health

Faculty of Fishery Sciences,

West Bengal University of Animal & Fishery Sciences,

Chakgaria, Kolkata 700094