How to Use TALOS-N
Use of TALOS-N is much the same as for TALOS and TALOS+:
Create a directory for the prediction session; all
subsequent commands will be executed from this directory.
Prepare the input table of chemical shift assignments
(for example "
myshifts.tab"), according to the
Run TALOS-N (
talosn) to perform the
database searches. Most commonly, this will simply require a command
talosn -in myshifts.tab
During the database search, a summary file "
will be created to store the 25 best database matches for all residues
in the target protein. Before exiting, a file "
will also be created, which includes an initial summary of the prediction
results. Additionally, three files "
predABP.tab" and "
will be created to store the calculated secondary chemical shifts used for
prediction, the ANN-predicted 324-state φ/ψ distribution
information and the predicted secondary structure, respectively.
The database search will typically take about 100 sec per 100 residues.
Run RAMA (
based jRAMA to inspect and adjust the predictions. The simplest
RAMA invocations are:
jrama -in myshifts.tab
jrama -in myshifts.tab -ref mystruct.pdb
During this inspection, you will:
Examine the φ/ψ distributions of the center residues
of the best 25 database matches for a given query residue, and
decide which ones should be included in the prediction, and which
are "outliers". (
NOTE: in the vast majority of
cases, the initial automated classifications performed by the current
version of the TALOS-N program should be acceptable with no manual
Classify the results for a given residue as "Strong",
"Generous", "Ambiguous", or (if a reference
structure is known) "Bad".
The file "
be adjusted along the way to reflect any changes made interactively, and
a new "pred.tab" summary file will be created on exiting. When
the above steps are completed, the final "
file will include the classification ("Strong", "Generous",
etc) and predictions (averages and standard deviations) for φ and ψ
at each residue.
Convert TALOS-N results to other formats, for use as
structural restraints, etc. TALOS-N package includes shell scripts such as
talosn2dyana.com" and "
" for this purpose, examples for using them are:
$TALOSN_DIR/com/talosn2dyana.com pred.tab > talos.aco
$TALOSN_DIR/com/talosn2xplor.com pred.tab > talos.tbl
offers similar features in its menu bar ("Tools").
Default criteria of angle contraints conversion: For "Strong"
predictions, the φ and ψ angles are set to <φ> +/- 2sd and
<ψ> +/- 2sd, where <φ> and <ψ> are the averaged TALOS-N predictions,
and 2sd is the larger of 20 deg or two standard deviations of the TALOS-N prediction.
For "Generous" predictions, the φ and ψ angles are set to <φ> +/- 3sd
and <ψ> +/- 3sd, where <φ> and <ψ> are the averaged TALOS-N
predictions, and 3sd is the larger of 30 deg or three standard deviations of the
Chemical shift data pre-check
Similar to TALOS+, TALOS-N includes a feature that pre-checks
chemical shift referencing and possible chemical shift errors
talosn -in myshifts.tab -check
It checks the referencing for
13Cβ, 1Hα and 13C' chemical shifts,
using the empirical correlation between certain sets of chemical shifts data
(Wang et al., 2005 J Biol NMR, 32:13-22). The estimated chemical shift
referencing offsets, as well as the chemical shifts which largely deviate
from their expected ranges, will be printed with the following format:
Chemical shift outlier checking...
64 E CB Secondary Shift: -3.800 Limit: -3.765
76 G C Secondary Shift: 4.250 Limit: 1.925 !
Chemical shift referencing checking...
Estimated Referencing Offset for CA/CB: 0.795 +/- 0.104 ppm (Size: 66)
Note that (1) a chemical shift referencing correction
is likely required when ever the estimated referencing error approaches
the average uncertainty in the database chemical shifts (~1.0 ppm for
13Cα/Cβ and 13C' shifts; ~0.3 ppm for
1Hα shifts), and/or the estimated referencing error
larger than five times the average fitting errors; (2) chemical shift
outliers, which fall far outside (>2-3 times of) the expected range
of secondary chemical shifts (and marked by "!"), are unlikely
to be correct (or like in the above example correspond to a C-terminal
carboxylate instead of a backbone carbonyl) and need to be checked
TALOS-N uses an option "
to automatically apply chemical shift offset correction if needed:
talosn -in myshifts.tab -offset
and an option "
-iso" to apply
correction to 13Cα/ 13Cβ chemical shifts
collected from a perdeuterated protein sample:
talosn -in myshifts.tab -iso
Exclusion of proteins from the database
Excluding one or more proteins from the database during
the TALOS-N database search can be performed by a command line such as:
talosn -in myshifts.tab -excl name1 name2 ...
name1" and "
etc. are the names of the proteins to be excluded (see the valid protein
names in the database "
Amino acid sequence based proten secondary structure prediction
By default, the amino acid sequence based proten secondary structure
prediction module is seamlessly implemented in TALOS-N as a complement to the chemical
shift based module and can bridge stretches in proteins that lack chemical shifts. This
amino acid sequence based module can be performed separately by a command line such as:
my_sequence.fasta" is the sequence input file with a standard
FASTA format. Please check the "
talosn_ss" script for all requirements
in order to run this module.