PACT is a computational pipeline for prediction of amyloid cross-interactions.

Description:

PACT uses template based modeling to build a model of amyloid aggregate consisting of both interacting peptides and assess if such structure is energetically favorable. A user provides the sequences of both potentially interacting amyloid fragments in TEXT format. The method can work with fragments of lengths between 14 and 45 amino acids.

Example input:

Protein1: IAPP
Seq1: KCNTATCATQRLANFLVHSSNNFGAILSSTNVGSNTY
Protein2: AmyloidB
Seq2: DAEFRHDSGYEVHHQKLVFFAEDVGSNKGAIIGLMVGGVV
Threshold: -256

Restrictions:

In case of longer proteins find the aggregation prone regions using AmyloGram or PATH. Alternatively, a sliding approach can be used. We recommend choosing window size based on the size of the aggregation-prone region of one of the proteins if it is known.
Be patient calculations can take some time!
If you want to use PACT on larger set of pairs consider using desktop version available at: https://github.com/KubaWojciechowski/PACT.
The current version of the method works only with 20 canonical amino acids and does not take into consideration postranslational modifications.
For most users, we recommend using a default threshold value. Lowering the threshold value will increase the specificity and decrease the sensitivity of the method.

Results:
When completed, your results will be available as zip file containing:

results.csv - file with the results of prediction
pair_0 - folder with generated models
energy.csv - file with enrgies of models
meta.csv - sequences length for internal use of PACT

Protein1:
Seq1:
Protein2:
Seq2:
Threshold: