Guidance on Predicting Protein-Peptide Complexes Using AlphaFold3

[ACIITB23]

I am currently facing an issue with predicting protein-peptide complexes. I have successfully installed AlphaFold3 locally and received the model parameters. While I am able to predict individual protein structures using the appropriate commands, I am encountering difficulties when trying to predict complexes. I have tried modifying the JSON files, but I was unable to run the predictions successfully.

Could you kindly provide the steps and commands required for predicting protein-peptide complexes? Additionally, I would appreciate guidance on how to handle predictions for more than 100 sequences.

Thank you very much for your assistance!

[zhanglzu]

This is a JSON file for predicting protein complexes that I used. Maybe it was not entirely correct. For reference only.

{
"name": "pos_v4",
"modelSeeds": [
10,
42
],
"sequences": [
{
"protein": {
"id": "E",
"sequence": "MSSTHSNNVGHPQSSPQGPLTEQQRAQQQYQIFENSLPKVSQSVYQMLLNEMVPLAMGIERQISGDVISSDSNVTSENGNINNMIKRLKIEEHHTVDIIRSHNLIHELYKADEEEKEKVLARLRNIGFQIGLKLSELLIFSNNPNLKFKEMDLLLIMKFICRDVWKQIFGKQIDNLKTNHRGTFYLLDYDYRPIQSFSLEEDAKNEELKMIEPFLEIPVGIIRGVLSSLGYSSEEVICLASFIDRPTDRPKTAFPKGVSFHVQVTMPQ"
}
},
{
"protein": {
"id": "P",
"sequence": "MVSTTQSRSLKAMGEEIWKNKTEKINTELFTLTYGSIVAQLCQDYERDFNKVNDHLYSMGYNIGCRLIEDFLARTALPRCENLVKTSEVLSKCAFKIFLNITPNITNWSHNKDTFSLILDENPLADFVELPMDAMKSLWYSNILCGVLKGSLEMVQLDCDVWFVSDILRGDSQTEIKVKLNRILKDEIPIGED"
}
}
],
"dialect": "alphafold3",
"version": 1
}