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Manual

How to use Agadir

Parameters

Agadir will be able to perform the calculation of one or more peptide sequences in one-letter format. The calculation will be done depending on the value of the following parameters:

  • N-terminus: No modification, Acetylation, Succynilation
  • C-terminus: No modification, Amidation
  • Ionic strength: between 0.001 and 1 M
  • Temperature: between 273 and 400 K
  • pH: between 1 and 14

Agadir offers also the possibility of screening a particular range of conditions for one parameter (ionic strength, temperature or pH). The screening will be done with step of 0.05M for the ionic strength, 1K for the temperature, or 0.2 for the pH.

Running Agadir from the command line

  1. Open a command line window and go to the directory where you have put the executable.
  2. Call Agadir as in the following example (use spaces, not tabs):
  • Agadir rl=G0 ct=N nt=N ph=7.4 te=303 io=0.05 seq=DNEWGYIAYHVSQDP
  • ct: Protection at the C-terminus: N (no) or Y (amidated)
  • nt: Protection at the N-terminus: N (no), A (acetylated) or S (succinilated)
  • ph: pH
  • te: Temperature (Kelvin)
  • io: Ionic strength

If you want to perform a screening, you will define the initial and final value of the parameter to be analyzed, i.e. te1/te2, ph1/ph2 or io1/io2.

Running Agadir interactively

  1. Open a command line window and go to the directory where you have put the executable.
  2. Call Agadir without any parameter as in the following example:
    Agadir
  3. Define if you need to perform a parameter screening or not
    Do you want to test a range of experimental conditions for your peptides?
    If yes type Y. Default, N
  4. Define the type of calculation
    Do you want to calculate the energy of a particular sequence segment, or do you want to determine the helical content? If yes type Y
  5. If you have responded Y in 4, you will define the sequence segment
    Give the number as an integer in the sequence of your N-cap (remembers your first residue in the sequence is zero)
  6. You will define if you want to get a global value or the detail for each residue
    Do you want to have the prediction at a residue level? If yes type Y. Default,N
  7. If you have responded Y in 3, you will define the parameter to screen
    Which of the three experimental parameters do you want to test? pH, Temperature or Ionic strength.
    Type 0 for none, 1 for pH, 2 for Temperature and 3 for Ionic strength
  8. Type the name of the file with the peptide names, conditions and sequence in one letter code and press Enter

The input file can have any name the user wants as long as it has less than 25 characters. Inside the file the user can place up to 10 sequences to be analyzed.
The format of the sequences to be run is as follows:

  • Name ct nt ph te io seq
  • Name: name of the sequence (less than 25 characters)
  • ct: Protection at the C-terminus: N (no) or Y (amidated)
  • nt: Protection at the N-terminus: N (no), A (acetylated) or S (succinilated)
  • ph: pH
  • te: Temperature (Kelvin)
  • io: Ionic strength seq: sequence of the peptide in one letter code.

Example

G0 Y A 5.3 276 0.1 AETAAAKFLRAHA
G1 Y A 5.3 276 0.1 AETAAAKFLRAHE
G2 Y A 5.3 276 0.1 AETAAAKFLRAHT
G3 Y A 5.3 276 0.1 AETAAAKFLRATT
G4 Y A 5.3 276 0.1 AETAAAKFLRAAA

Agadir output

The output of Agadir will be directly in the command prompt or in a text file depending on the type of calculation executed.

If you run Agadir as command line without any parameter screening, the output will just be the value.

If you run Agadir as command line with a parameter screening, the output will be the list of values depending on the parameter:
Temperature 276.00 29.05
Temperature 277.00 30.46
Temperature 278.00 29.75
Temperature 279.00 29.05
Temperature 280.00 28.36
Temperature 281.00 27.69
Temperature 282.00 27.02
Temperature 283.00 26.37
Temperature 284.00 25.73
Temperature 285.00 25.10
Temperature 286.00 24.49
Temperature 287.00 23.88
Temperature 288.00 23.29
Temperature 289.00 22.71
Temperature 290.00 22.14
Temperature 291.00 21.59
Temperature 292.00 21.05
Temperature 293.00 20.52
Temperature 294.00 20.00
Temperature 295.00 19.49
Temperature 296.00 19.00
Temperature 297.00 18.52
Temperature 298.00 18.05
Temperature 299.00 17.59
Temperature 300.00 17.14
Temperature 301.00 16.71

If you have run Agadir in the interactive mode, you will get a value directly in the command prompt and an output file with the extension .out presenting for each sequence the sequence name and the value associated.
If you have requested the prediction as residue level, you will get an output file with the extension .HEL presenting for each position:

  • Residue Level Helix Content
  • Residue level N-Cap probability
  • Residue level C-Cap probability
  • Residue level probability to start H-Staple
  • Residue level probability to start Schellman motif
  • 1HA Conformational Shift
  • 13CA Conformational shift
  • Coupling Constants

res, aa, Hel, Ncap, Ccap,Hstaple,Schellm, CaH, 13Ca, JaN
00, B, 0.00, 6.86, 0.00, 0.00, 0.00, 0.00, 0.00, 0.00
01, A, 6.86, 0.88, 0.00, 0.00, 0.00, -0.01, 0.13, 5.67
02, E, 7.74, 1.06, 0.00, 0.00, 0.00, 0.00, -0.13, 6.04
03, T, 8.80, 39.13, 0.00, 0.00, 0.00, -0.02, -0.47, 7.62
04, A, 47.93, 0.40, 0.00, 0.00, 0.00, -0.10, 0.91, 5.32
05, A, 48.18, 0.29, 0.15, 0.00, 0.00, -0.10, 0.92, 5.32
06, A, 48.26, 0.15, 0.21, 0.00, 0.00, -0.11, 0.92, 5.35
07, K, 47.08, 0.07, 1.33, 0.00, 0.00, -0.17, 1.11, 5.94
08, F, 42.01, 0.06, 5.14, 0.00, 0.00, -0.25, 1.46, 6.55
09, L, 40.79, 0.06, 1.27, 0.00, 0.00, -0.19, 0.76, 6.03
10, R, 39.22, 0.00, 1.63, 0.00, 0.00, -0.16, 1.23, 6.04
11, A, 36.08, 0.00, 3.14, 0.00, 0.00, -0.11, 0.75, 6.25
12, H, 14.01, 0.00, 22.07, 0.00, 0.00, -0.12, 1.30, 8.46
13, A, 9.03, 0.00, 4.97, 0.00, 0.00, -0.10, 0.27, 6.16
14, U, 0.00, 0.00, 9.03, 0.00, 0.00, 0.00, 0.00, 0.0