Dear Daniel,
Multiple templates do improve the prediction accuracy as compared to the single best templates. This has been published in several papers. This has been reviewed correctly here
Anna Tramontano: Protein Struture Prediction: Concepts and Applications Wiley-VCH; 2006.
But here is a trick too, first of all you didn't mention what you actually used. Please answer these queries to help you practically with the best possible answer.
1. Did you use salign_iterative/salign_multiple?
2. What was the length of your sequence?
3. Did you do increased sampling?
All the Scores that you discussed won't allow you to rank templates and select their correct set.
Hence, it is beneficial if you try to take the correct set of a few biologically related templates.
Good Luck,
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <>
To: "modeller usage" <>
Sent: Thursday, July 21, 2011 12:59:26 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 103
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Today's Topics:
1. Re: ModWeb details -> Modeller? (Modeller Caretaker)
2. Re: Help with modeller 9.9 in windows (Modeller Caretaker)
3. Multiple Sequence Alignment vs Single Alignment (Daniel Li)
----------------------------------------------------------------------
Message: 1
Date: Mon, 18 Jul 2011 12:13:13 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] ModWeb details -> Modeller?
To:
Cc:
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 7/17/11 10:57 PM, richard k belew wrote:
> i've done a couple of runs using the ModWeb server, and i'm wondering
> how to recapitulate its results using Modeller directly? ModWeb gives
> a .pdb file as a result, with a header that tells the template it
> selected, and regions in it that were used for modeling. but:
> - what method is used for selecting this template?
> - is it possible to get the alignment that was used?
If you asked for your results to be uploaded into ModBase, you can
download the alignment file for each model from that web interface. The
header of the alignment file specifies the method that was used to find
the template (e.g. sequence-sequence, sequence-profile).
If you instead chose to have the models sent directly to you, the
alignment file isn't available. But it might still be on our system
somewhere - if you email with your ModWeb job ID we
can see if we can find it for you.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 2
Date: Mon, 18 Jul 2011 12:21:16 -0700
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Help with modeller 9.9 in windows
To: "Greene, Brandon Lee" <>
Cc: "" <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 7/18/11 7:22 AM, Greene, Brandon Lee wrote:
> There are three inorganic residues in the first chain and one in the
> second placed as "." in my ali file.
Your alignment file does not match the PDB. Modeller reads the residues
sequentially, so what it will see is
- A chain amino acids
- B chain amino acids
- A chain ligands
- B chain ligands
So your sequence should also be in this order (XXXXXX/XXXXXX/.../.).
Alternatively, you can edit the PDB file to place the A chain ligands
immediately after the A chain amino acids and leave your alignment
unchanged.
> Using this structure and the template ali file to do the alignment (w/
> salign) I get poor alignment in the PAP file, but not in the PIR file???
> (P/---XXXX instead of P---/XXX in PAP).
Those two alignments are identical. Since neither gaps nor chain breaks
are "real" residues, their relative ordering is irrelevant - it only
matters which "real" residues (amino acids or ligands) they come between.
> "No aligned template residues for BLK residue; number of templates: 1
> Make sure that each BLK residue in your target sequence is aligned with
> your templates..."
Just like it says, a BLK (".") residue in the target sequence must be
aligned with a residue in the template. Usually this means you need a
"." residue in the template in the same place as the "." in the target.
You can't align a "." with a chain break or gap, because "." means to
copy the aligned residue directly from the template to the target, so it
needs a "real" residue to copy from.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 3
Date: Thu, 21 Jul 2011 00:16:06 -0700 (PDT)
From: Daniel Li <>
Subject: [modeller_usage] Multiple Sequence Alignment vs Single
Alignment
To:
Message-ID:
<>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I have been reading about modeller usage for awhile and ran some tests with different models from the dual specificity phosphatase family. However, whenever I run the modelling with salign for multiple templates, my GA341 score is many folds lower (under 0.1) and the dope score/molpdf scores are lower as well compared to just a single template.?The templates that I use all give me a decent 50%+ identity based on output from build profile and I generally use 3 templates for my multiple template modeling.From reading it seems as if multiple templates should usually generate better scores but running 3 trials of 600 with different sets of templates for different proteins I still get better results from my single template models. So is there something I have to manipulate with the scripts and parameters?I'm sorry for the vague question because I'm not too sure what kind of additional information to provide but I hope someone can provide me with more insight
into this.
Thank you!
Daniel
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