Benn, CASP winners used HMM based profiles for target as well as template to rank and consider the template hits. Their approach is better when the target sequence identity to known templates lie below the twilight zone mark.
Ashish
Ashish Runthala,
Lecturer, Structural Biology Cell,
Biological Sciences Group,
BITS, Pilani
Rajasthan, INDIA
----- Original Message -----
From: "modeller usage-request" <>
To: "modeller usage" <>
Sent: Tuesday, March 1, 2011 11:41:02 PM GMT +05:30 Chennai, Kolkata, Mumbai, New Delhi
Subject: modeller_usage Digest, Vol 10, Issue 42
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Today's Topics:
1. Re: about model rank (Modeller Caretaker)
2. Re: Regarding Salign (Modeller Caretaker)
3. Re: No template... (Modeller Caretaker)
4. No template... (Anna Marabotti)
----------------------------------------------------------------------
Message: 1
Date: Tue, 01 Mar 2011 08:10:37 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] about model rank
To: modeller usage <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 3/1/11 12:23 AM, Ashish Runthala wrote:
> NEVER USE DOPE ALONE TO RANK MODELS. ONLY DOPE IS NOT A GOOD SELECTION MEASURE.
Such a strong statement needs to be backed up by a publication...
particularly given that it is contradicted by both your next sentence
and our own study (Prot Sci 17, 1881-1893, 2008).
> Use normalized_dope
Normalized DOPE is derived from the raw DOPE score. Thus the ranking of
models, given the same sequence, will be the same with DOPE or
normalized DOPE.
However, since raw DOPE is an "energy", you should certainly not use it
to rank models that differ in sequence. For that, normalized DOPE would
be more appropriate.
> or GDT to rank models/Clusters/Hybrid Models.
GDT is a structural measure, like RMSD, so it requires another structure
to compare against. This makes it useless for assessing comparative
models unless you already know the answer (as in CASP).
Ben Webb, Modeller Caretaker
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http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 2
Date: Tue, 01 Mar 2011 08:12:08 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] Regarding Salign
To: Ashish Runthala <>
Cc: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 2/28/11 2:33 AM, Ashish Runthala wrote:
> How does align2d_mult actually adds the target sequence onto the
> aligned templates ali file.
The algorithm is fully described in Prot. Eng. Des. & Sel. 19, 129-133.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 3
Date: Tue, 01 Mar 2011 08:19:46 -0800
From: Modeller Caretaker <>
Subject: Re: [modeller_usage] No template...
To: Marco Sette <>
Cc: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 3/1/11 6:31 AM, Marco Sette wrote:
> I have a protein consisting of a C-terminal and N-terminal region.
> While for the C-terminal one I have a good template either Modeller
> or Blast don't suggest templates for the N-terminal one. I have some
> suggestion using Modweb (which search performs Modweb?) but not very
> good. Could ou suggest me a website to search for a template? I
> looked at the mailing list (very long...) but seems this question has
> not been posed. Many thanks,
Since Modeller is a package for comparative modeling, if you don't have
a template, you cannot model that region of your model.
I don't know what you mean by "Modeller ... doesn't suggest templates"
since Modeller doesn't suggest templates for you. Perhaps you mean you
are doing a sequence-sequence search to look for templates (step 1 of
the basic tutorial) and you didn't find any? BLAST does essentially the
same thing - except that it's using an approximation rather than "real"
dynamic programming, so it runs faster - so is also unlikely to find a
template if this search doesn't work.
ModWeb supplements this basic sequence-sequence search with more
sensitive profile-based searches (it also tries PSI-BLAST, which is a
similar method). But there are many other methods available to search
for templates - e.g. HMM-based. One thing you could do is look at the
best performers for the last CASP contest and see how they detect
templates - some of those are available as web servers.
Ben Webb, Modeller Caretaker
--
http://www.salilab.org/modeller/
Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage
------------------------------
Message: 4
Date: Tue, 01 Mar 2011 16:45:45 +0100
From: Anna Marabotti <>
Subject: [modeller_usage] No template...
To:
Message-ID: <>
Content-Type: text/plain; charset=us-ascii
Dear Marco,
have you tried to perform the search for a template using fold recognition
tools such as GenThreader, 3D-PSSM and so on? They use a different criterium
to find a template with respect to BLAST and PSI-BLAST, and they are
effective in finding templates when the similarity of sequences is low.
Cheers
Anna
Date: Tue, 1 Mar 2011 14:31:22 +0000 (GMT)
From: Marco Sette <>
Subject: [modeller_usage] No template...
To: modeller <>
Message-ID: <>
Content-Type: text/plain; charset=iso-8859-1
Dear all,
I have a protein consisting of a C-terminal and N-terminal region. While for
the C-terminal one I have a good template either Modeller or Blast don't
suggest templates for the N-terminal one.
I have some suggestion using Modweb (which search performs Modweb?) but not
very good.
Could ou suggest me a website to search for a template?
I looked at the mailing list (very long...) but seems this question has not
been posed.
Many thanks,
Marco
Dr.Marco Sette, Ph.D.
Department of Chemical Sciences and Technology
University of Rome, "Tor Vergata"
via della Ricerca Scientifica, 00133, Rome, Italy
e-mail:
e-mail:
Tel.: +39-0672594424
Fax: +39-0672594328
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