How to use Agadir
To submit a job to Agadir, log in the calculation part using the login button in the right bottom. Then fill-in the input form and proceed to next page, etc. You will reach a final page that resumes all the input information and allows you to run the calculation. You can submit one or more peptide sequences in one-letter format. Sequences should be separated by one return character. Spaces and tabulations are automatically removed. Only standard amino acids are accepted. Agadir accepts two modifications at the N-terminus (acetylation or succynilation), and one at the C-terminus (amidation). Just choose the desired option in the input form. You can use only one set of parameters: temperature, ionic strength (calibrated for NaCl) and pH, or explore a particular range of conditions for one parameter.
In the latter case the intervals between any two values are:
- Ionic strength 0.05 M
- Temperature 1 K
- pH 0.2 units
When setting the conditions for these parameters please be aware that the allowed ranges are:
- Ionic strength between 0.001 and 1 M
- Temperature between 273 and 400 K
- pH between 1 and 14
Output of the prediction at the residue level is available only when submitting no more than ten peptide sequences, and without any screening of conditions. Hstaple is the Hydrophobic Staple motif, Schellman is the Shellman motif, CaH are the expecte chemical shifts of the Calpha proton, 13Ca are the alpha Carbon 13 chemical shifts, JaN is the Jalpha--nitrogen coupling.
Intellectual property issues are handled by EMBLEM. Only executables are available for download from our website, based on a material transfer agreement (mta) with EMBLEM. The source code is protected.
When refering to Agadir, please reference the following papers
Muñoz, V. & Serrano, L. (1994a)
Elucidating the folding problem of helical peptides using empirical parameters.
Nature: Struct. Biol. 1, 399-409
Muñoz, V. & Serrano, L. (1994b)
Elucidating the folding problem of a-helical peptides using empirical parameters, II. Helix macrodipole effects and rational modification of the helical content of natural peptides.
J. Mol. Biol 245, 275-296
Muñoz, V. & Serrano, L. (1994c)
Elucidating the folding problem of a-helical peptides using empirical parameters III: Temperature and pH dependence.
J. Mol. Biol 245, 297-308
Muñoz, V. & Serrano, L. (1997)
Development of the Multiple Sequence Approximation within the Agadir Model of a-Helix Formation. Comparison with Zimm-Bragg and Lifson-Roig Formalisms.
Biopolymers 41, 495-509
Lacroix, E., Viguera AR & Serrano, L. (1998)
Elucidating the folding problem of a-helices: Local motifs, long-range electrostatics, ionic strength dependence and prediction of NMR parameters.
J. Mol. Biol. 284, 173-191
Agadir1s and 2s have been succesfully used to stabilize proteins through helix stabilisation:
- Villegas, V., Viguera, A.R., Avilés, F.X. & Serrano, L. (1996).
Stabilisation of proteins by rational design of a-helix stability using helix/coil transition theory.
Folding & Design, 1,29-34.
- Muñoz, V. & Serrano, L. (1996).
Local vs non-local interactions in protein folding and stability. An experimentalist point of view.
Folding & Design. 1, R71-R77.
- López-Hernández, E., Cronet, P., Serrano, L. & Muñoz, V. (1997).
Kinetics of CheY mutants with enhanced native a-helix propensities.
J. Mol. Biol. 266, 610-620.
- Viguera, A.R., Villegas, V., Avilés, F.X. & Serrano, L. (1996).
Favourable native-like helical local interactions can accelerate protein folding.
Folding & Design, 2, 23-33.