predicting secondary structure of proteins locally on unix system

[Nermin Celik]

Hello,

Need to determine the secondary structure of a large number of protein dataset.
Can someone please recommend a software that can be run locally on a unix system,
and analyzed with ease.

Thank you in advance.

NC

[Guy Yachdav]

Dear Nermin,

Our secondary strcuture, solvent accessibility and transmembrane helices  predictor - PROFPhd is freely available for both Debian (e.g. Ubuntu) ad RPM (RedHad, CentOS, SUSE) based linux systems. More details can be found here:

https://rostlab.org/owiki/index.php/Profphd

https://rostlab.org/owiki/index.php/Packages#profphd

Please let me know if you have additional questions. 

Best, 

Guy

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[Guy Yachdav]

Dear Nermin,

Our secondary strcuture, solvent accessibility and transmembrane helices  predictor - PROFPhd is freely available for both Debian (e.g. Ubuntu) ad RPM (RedHad, CentOS, SUSE) based linux systems. More details can be found here:

https://rostlab.org/owiki/index.php/Profphd

https://rostlab.org/owiki/index.php/Packages#profphd

Please let me know if you have additional questions. 

Best, 

Guy

On Jun 27, 2011, at 2:43 AM, Nermin Celik wrote:

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Guy Yachdav

gyac...@predictprotein.org

[Liza]

Hello NC,
I have been used Phyre http://www.sbg.bio.ic.ac.uk/~phyre/ on windows.

2011/6/27 Nermin Celik <n.ce...@gmail.com>

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[Becker, Argentina]

Hi everybody,

I am working with a protein that binds GM1, a ganglioside. When incubated only with the pentasaccharide portion of GM1, the protein does not bind to the sugar. My observation is that the lipid part plays the key role in binding. I want to use other lipids like GM2, GM3, GD1a.... to see if my protein shows any binding to other lipids. Does anybody know about a lipid microarray (like the one they have for sugars at the Consortium for Functional glycomics) I can send my protein to or a lipid screen that I can buy?

This info will be very useful to me. Thank you very much for your help.

Jenn

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From: predictprot...@googlegroups.com [predictprot...@googlegroups.com] on behalf of Liza [lizaff...@gmail.com]
Sent: Thursday, July 07, 2011 7:23 AM
To: predictprot...@googlegroups.com
Subject: Re: [predictprotein-science:597] predicting secondary structure of proteins locally on unix system

[Sarka Tumova]

Hi Jenn,

Echelon Biosciences sells some lipid arrays, although I do not think those include gangliosides.  You can also make lipid arrays yourself by spotting different lipid concentrations (in chloroform:methanol) onto a PVDF membrane, using for example following paper as a guideline:

Hayashi T, Fujimoto M.: Detergent-resistant microdomains determine the localization of sigma-1 receptors to the endoplasmic reticulum-mitochondria junction. Mol Pharmacol. 2010 Apr;77(4):517-28.  Hope this helps.

Good luck,

Sarka

 

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[santosh kathwate]

hi friends,

i hv a protein sequence i want i tried to blast it against candida genome but i could not got any similar sequence in it. my intention is to find similar sequence in candida genome but i could nt find any similar sequence. is there any tool like blast, which can use candida secondary sequence database for searching similar pattarn in for my sequence.

Mr. Santosh H. Kathwate,
CSIR-JRF,
School of Life Sciences,
S.R.T.M.University, Nanded.
Nanded (MS) 431 606, India.