TALOS

Introduction

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

For detailed information please check the TALOS and TALOS+ web sites.  For installation questions and other support, you can also e-mail Yang Shen.

There is a web-based server available from Ad Bax's TALOS+ web site: http://spin.niddk.nih.gov/bax/software/TALOS+/index.html
This is probably the best thing to use since you can be sure that the Talos+ chemical shift database is the most recent.

Generating TALOS dihedral angle constraints with CYANA (UB)

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

 read prot XXXX.prot 
 taloslist XXXX

1. This will create the TALOS input file XXXX.tab. In this file rename all "H" atoms to "HN".
2. In a UNIX shell run
   

   talos+ -in XXXX.tab

   This will create a file pred.tab, which includes an initial summary of the prediction results.

3. In a UNIX shell run
   

   rama+ -in XXXX.tab

   Here you can examine phi and psi distributions, choose database matches to be used in calculating predictions, and classify prediction results as Good, Ambiguous or Unclassified / New. See below for the guidelines for classifying prediction. Save your modifications in a new file, for example, talos.tab.

4. Start CYANA and type:
   

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

   write aco talos.aco

   
   

talosaco.cya macro

The talosaco macro is invoked as:

talosaco file [factor [width]]

Here file is the TALOS prediction output, width is the threshold minimum width for PHI/PSI angle distributions, and factor is used to scale the width of a distribution when creating an angle constraint. Both width and factor arguments are optional. By default, width=20.0 and factor=2.0.

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.

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

Interactive Refinement of TALOS Predictions

Guidelines for refining the TALOS output:

• Classify prediction as Good 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 phi < 0, and the one outlier also lies in phi < 0 half of the map
  • Or 9 out of 10 of the best database matches fall in a consistent region with phi > 0
• Accept predictions which are classified as Good, 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 talos.aco file.

During structure refinement you can refine TALOS predictions against a preliminary structure.

vina.tcl -in XXXX.tab -ref XXXX.pdb -auto

and

rama.tcl -in XXXX.tab -ref XXXX.pdb

The XXXX.pdb file must have only one conformer. Thus, you may need to analyze the angle distributions in a molecular graphics package (e.g. MOLMOL).

Element	PHI	PSI
α-helix	-60	-45
β-sheet	-140	135

Recommendations for Using TALOS constraints in CYANA calculations

• The recommended conservative approach is to apply TALOS constraints for regular secondary structure elements (as predicted by CSI, for example) only, excluding the flanking residues.
• If the NOE constraint network is quite dense, the best approach is to run an automated CYANA calculation without TALOS constraints and then verify the TALOS predictions for consistency with the PHI/PSI angle distributions in the resulting structures. The validated TALOS constraints can then be used in subsequent structure calculations.
• TALOS constraints may be used from the beginning to improve convergence of automated CYANA calculations in challenging cases, such as systems with sparse NOE, or homodimeric proteins.

Using TALOS and TALOS+ at CABM

Preparing for a TALOS+ run

• Make a sub-directory in your project for TALOS.
• you will need the following files in your directory:
• a bmrb file in 2.1 format.  Here is an example.
• BMRBParsing.pm:  BMRB parser
• Tab4Talos.pl:  perl script to prepare input file for TALOS
• talos2dyana_taloserrors.pl:  perl script to prepare a CYANA .aco file
• Run the following command:

	Tab4Talos.pl [.bmrbf] [input4Talos]

This make an input chemical shift list for TALOS.  Here is an example.

Running TALOS+ and making a dihedral angle constraint file

• Next run talos+:

	talos+ -in [input4Talos]

This makes a number of output files including the pred.tab. 

• Next, edit the pred.tab and comment out (#) any lines that do not have the "10 Good" comment. 
• Finally, run the talos2cyana perl script to make a CYANA .aco file with only the results classified as "10 Good", and using the phi and psi errors given by TALOS.  They user can modify this script to make his/her own error limits (i.e., +/- 20 or 30).

	perl talos2dyana_taloserrors.pl pred.tab [output.aco]