Re: [modeller_usage] How to get Secondary Structure in Alignment file

On 27 March 2011 10:05, Ashish Runthala <">> wrote:

Dear Thomas,
I will write it clearly this time.
Take simplest case.Suppose, I have a structural/sequence alignment of 3 templates against a target sequence. Now, as modeller predicts tertiary conformation for the target sequence, it surely predicts the alignment based secondary structure information against all the templates. So now i want that specific secondary structure information along with the alignment file for the aligned templates against the target sequence.
Now my C script will take on this alignment file to generate the representative best possible optimum alignment for the considered target sequence. These models in my tried iterations for the CASP8 targets gave excellent results.

So if I understand correctly, your script creates alternative alignments, then runs Modeller to build a model of the target from each alignment, it reads the secondary structure (SS) from each model, and based on this SS it judges which alternative alignment is the optimum. Is this how it works? Can you elaborate on the algorithm? What are the criteria to select the optimum alignment and what is the answer you seek from the mailing list?

I think i made myself clear this time.
By the way, what you are working on. I think you are also working on the same topics. What you have redefined? I am interested to know that.

I've been working on optimization at the alignment level in the past, but in my approach the selection of the optimum alignment and template combination is based on the overall native-likeness of the resulting homology models, not just the secondary structure of the target. More specifically, I create homology models at several levels of optimization and refinement from alternative alignments and different template combinations. The resulting models are sorted according to the DOPE-HR score, and the best of them undergo side-chain optimization with SCWRL4, and extensive stereochemical tests with the programs PROCHECK and WHAT_CHECK to select the best of them. The whole procedure is streamlined and parallelized with a combination of bash and python scripts. However, it has been tested only on my cases and a few CASP9 targets. More details can be found at:

https://sites.google.com/site/hmopalpipeline/home (I will update the website tomorrow)

Thanks in advance,

Ashish

Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA

----- Original Message -----
From: "Thomas Evangelidis" <">>
To: "Ashish Runthala" <">>

Cc: "modeller usage" <">>
Sent: Saturday, March 26, 2011 6:06:02 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment file

On 26 March 2011 07:47, Ashish Runthala < "> > wrote:

Dear Thomas,
You mentioned the free tools in details. I appreciate that. But what i don't understand is to manually call everyone, and then keep on doing it, is tedious but fun it is.

So if I get it right this time, you didn't ask what commercial free tools are available to display your sequence alignment along with the secondary structure, is that correct? Could you please be more careful with your syntax cause it's kind of difficult to follow you.

I had a query that template secondary structure information is there in templates, but with indels, that may be disturbed. I mean the native information is deteriorated.

So if based on indels, available in current alignment, if i can link directly to a python script. So that my next programme to generate the optimal alignment will become successful, as i did all of these several times manually, to design the algorithm to generate best representative alignment.

So you want to write a python script that can cope with indels inside SSEs. Namely, given a structure-based alignment between your target and templates, you want to select which of the following alignments is the optimum:

target > HCSIHHSC
Template1> HCSIHISC
Template2> HCSHHISC
-------------------------------------------------------
target > HCS-IHHSC
Template1> HCS-IHISC
Template2> HCSH-HISC
-------------------------------------------------------
target > HCSI-HHSC
Template1> HCS-IHISC
Template2> HCS-HHISC

etc.

Is this what you seek?

Will you please elaborate this time.

Thanks,
Ashish

Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA

----- Original Message -----
From: "Thomas Evangelidis" < "> >
To: "Ashish Runthala" < "> >
Cc: "modeller" < "> >
Sent: Friday, March 25, 2011 4:50:42 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: Re: [modeller_usage] How to get Secondary Structure in Alignment file

Maestro from Schrodinger can display both the predicted secondary structure elements (SSE) of the target and the SSE of the templates above the alignment dynamically (namely if you change the alignment the SSEs are changed accordingly).

Alternatively you can use the following commercial free tools:

ESPript ( http://espript.ibcp.fr/ESPript/ESPript/ ): can create an image of your alignment with the SSEs of your templates above it. No SSE of the target is displayed though.

MolIDE ( http://dunbrack.fccc.edu/molide/index.php ): I have the notion that this alignment editor (and not only) can display both the predicted SSE of the target and the SSE of the templates. However, I didn't manage to run it yet due to compilation problems. I intend to give it a try in the near future.

STRAP ( http://3d-alignment.eu/ ): it can do both but the GUI is not handy in Linux (windows and fonts are unequal, etc.).

Finally you can add a row with the secondary structure (as you wrote it in your email) above each sequence in your alignment editor. I prefer Jalview and like to play around with groups and colors. See the attached image for an example. SSE of your templates can be retrieved from PDB (e.g. http://www.pdb.org/pdb/explore/sequenceText.do?structureId=2IXF&chainId=A ) whereas the SSE of your target can be predicted by Jpred3 ( http://www.compbio.dundee.ac.uk/www-jpred/ ).

HTH,

Thomas

On 25 March 2011 05:47, Ashish Runthala < "> > wrote:

Dear Modellers,
Suppose i have two templates, and a target sequence. Instead of sequence alignment based file, i want to consider the secondary structure information, like given below

Template1> HCSIHISC
Template2> HCSHHISC

H=Helix, C=Coil, S-Strand, I=Indels

Is it possible to get the alignment in this case for multiple templates against the target sequence( whose structure can also be represented as best aligned folds)

Thanks
Ashish

Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
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======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: ">

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website: https://sites.google.com/site/thomasevangelidishomepage/

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======================================================================

Thomas Evangelidis

PhD student

Biomedical Research Foundation, Academy of Athens

4 Soranou Ephessiou , 115 27 Athens, Greece

email: ">

">

website: https://sites.google.com/site/thomasevangelidishomepage/