View source for TALOS

== '''Introduction'''  ==

TALOS (Torsion Angle Likelihood Obtained from Shift and sequence similarity) is a database system for empirical prediction of <tt>phi</tt> and <tt>psi</tt> backbone torsion angles from five kinds (HA, CA, CB, CO, N) of chemical shifts for a given protein sequence (Ref. 1).&nbsp; In 2009, the Bax laboratory released a new and improved version of the program called TALOS+ (Ref. 2).<br> 

For detailed information please check the [http://spin.niddk.nih.gov/NMRPipe/talos/ TALOS] and [http://spin.niddk.nih.gov/bax/software/TALOS+/index.html TALOS+] web sites.&nbsp; For installation questions and other support, you can also e-mail [mailto:shenyang@niddk.nih.gov Yang Shen]. 

== '''Using TALOS'''  ==

#Create a subdirectory (for example, <tt>structure/cyana21/talos</tt>) and copy the latest sequence and atom list files there. It is convenient to have them named <tt>XXXX.seq</tt> and <tt>XXXX.prot</tt>, where <tt>XXXX</tt> is an NESG target ID or other protein name. When using CARA, export the chemical shifts as an atom list file in this directory. 
#Create and init.cya in this directory as described in "[[NESG:CYANAInitFile|Creating an init.cya file for CYANA 2.1]]" or copy a previously used file. 
#Start CYANA and type:

      read prot XXXX.prot
      taloslist XXXX

#This will create the TALOS input file <tt>XXXX.tab</tt>. In a UNIX shell run <tt>talos.tcl -in XXXX.tab</tt>. During the database search, a series of files <tt>pred/res*.tab</tt> will be created. Each one of these files tallies the 10 best database matches for a given residue in the target protein. Before exiting, <tt>talos.tcl</tt> calls <tt>vina.tcl</tt> to create a file <tt>pred.tab</tt>, which includes an initial summary of the prediction results. The database search will typically take about 10-60 sec per residue in the target. 
#In a UNIX shell run <tt>rama.tcl -in XXXX.tab</tt>. Here you can examine <tt>phi</tt> and <tt>psi</tt> distributions, choose database matches to be used in calculating predictions, and classify prediction results as <tt>Good</tt>, <tt>Ambiguous</tt> or <tt>Unclassified</tt> / <tt>New</tt>. See below for the guidelines for classifying prediction. Save your modifications in a new file, for example, <tt>talos.tab</tt>. 
#Start CYANA and type:

    talosaco pred    #or "talos.tab" -- use the appropriate filename
    write aco talos.aco

See also the <tt>~/demo/details/TalosAngleRestraints.cya</tt> example script in your local CYANA 2.1 installation. 

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== '''Manual Refinement of TALOS Predictions'''  ==

Guidelines for refining the TALOS output: 

*Classify prediction as <tt>Good</tt> only if 
**All 10 best database matches fall in a "consistent" region of the Ramachandran map 
**Or 9 out of 10 best database matches fall in a consistent region with <tt>phi &lt; 0</tt>, and the one outlier also lies in <tt>phi &lt; 0</tt> half of the map 
**Or 9 out of 10 of the best database matches fall in a consistent region with <tt>phi &gt; 0</tt> 
*Accept predictions which are classified as <tt>Good</tt>, whose residues are in beta-sheets or helices according to CSI (excluding the first and the last residue of a secondary structure element).

For ''de novo'' structure determination it is recommended to take the automatically generated TALOS constraints. Angular constraints outside of secondary structure elements (as determined by CSI) can be commented out in the <tt>talos.aco</tt> file. 

During structure refinement you can refine TALOS predictions against a preliminary structure. 
<pre>vina.tcl -in XXXX.tab -ref XXXX.pdb -auto</pre> 
and 
<pre>rama.tcl -in XXXX.tab -ref XXXX.pdb</pre> 
<br> The <tt>XXXX.pdb</tt> file '''must''' have only one conformer. Thus, you may need to analyze the angle distributions in a molecular graphics package (e.g. MOLMOL). 

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{| border="1"
|-
| Element 
| PHI 
| PSI
|-
| α-helix 
| -60 
| -45
|-
| β-sheet 
| -140 
| 135
|}

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== '''Description of talosaco.cya Macro'''  ==

Invoked as: 
<pre>talosaco file [factor [width]]</pre> 
Here <tt>file</tt> is the TALOS prediction output, <tt>width</tt> is the threshold minimum width for <tt>PHI/PSI</tt> angle distributions, and <tt>factor</tt> is used to scale the width of a distribution when creating an angle constraint. Both <tt>width</tt> and <tt>factor</tt> arguments are optional. By default, <tt>width=20.0</tt> and <tt>factor=2.0</tt>. 

This macro will create angle constraints for a given residue only if the prediction is classified as "Good" and the residue is not a proline. 

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== '''References'''  ==

<font face="Arial,Helvetica">[http://spin.niddk.nih.gov/bax/software/TALOS/info.html Protein backbone angle restraints from searching a database for chemical shift and sequence homology]</font> 

<font face="Arial,Helvetica">Gabriel Cornilescu, Frank Delaglio, and Ad Bax</font> <font face="Arial,Helvetica">''J. Biomol. NMR,'' '''13''' (1999) 289-302</font> 
<blockquote><font face="Arial,Helvetica">[http://www.springerlink.com/content/w7wgg13587233964/fulltext.html TALOS+: A hybrid method for predicting protein backbone torsion angles from NMR chemical shifts]</font><br> <font face="Arial,Helvetica">Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Bax</font> <br> <font face="Arial,Helvetica">[http://dx.doi.org/10.1007/s10858-009-9333-z ''J. Biomol. NMR,'' 44(2009):213-223]</font> </blockquote> 
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<br> -- AlexEletski - 7 Jun 2007 

-- Updated by JimAramini - 11 Nov 2009 

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