POSEIDON

Welcome to POSEIDON: Peptidic Objects SEquence-based Interaction with cellular DOmaiNs. This webserver allows the user to input solely a peptide sequence and attain an in silico prediction for its uptake value in different cell lines. The uptake values considered are scaled in the form of log₁₀(Uptake). Please cite A.J. Preto, Ana B. Caniceiro, Francisco Duarte, Hugo Fernandes, Lino Ferreira, Joana Mourão and Irina S. Moreira 2023.

Submit

Input your peptide in the upload box, check the the rest of the submission forms for concentration, temperature, and incubation time, atypical changes in your peptide such as cargo and sequence anomalies, select the tissue and click submit. The only mandatory fields are the peptide sequence, e-mail and run name, the remaining fields will be fed the default values if left unchanged. The protein sequence should only contain the amino acid single letter codes. You will be directly sent to your results page, which might take some time to finish. Please, also fill-up your email address and an appropriate name for the run. An email will be sent to you with the results link.

Insert you peptide sequence, using only the 20 commonly occurring amino acids.

Type the concentration (μM) as well as the time (minutes), and the temperature (℃). If you do not, the most frequently occuring values in the original dataset will be selected, corresponding to the default in the dropdowns. Finally, check the "Cyclic" checkbox if your peptide is or contains cyclic sections (default value is non-cyclic).

Concentration (μM)

Time (minutes)

Temperature (℃)

Cyclic

If you have amino acids that are not the naturally occurring L-amino acids, insert their positions in the "D-amino acids" box, separating the input with commas (e.g. 1,5,9). Furthermore, if your peptide has additional cargos, select up until two cargos from the available dropdowns. If your cargo is not in the dropdown, we advise either selecting a similar one from the dropdown or leaving the default empty values.

D-amino acids

Cargo 1

Cargo 2

If your peptide contains anomalous substituted amino acids insert their positions in the "Anomalous positions" box, separating the input with commas (e.g. 1,5,9). Next, select the substituting amino acid from the dropdown.

Anomalous positions

Anomalous substitution

Select your tissue, which will be matched with the available cell lines. Otherwise, keep the default "All" to predict peptide uptake for all available cell lines.

Tissue

Finally, input you email, make sure your email is valid, otherwise the only way to access the results is through the submission page. Also ensure you have a simple and representative run name.