PANDORA

PANDORA is a fast, modularized and highly flexible anchor-restrained modelling pipeline for generating peptide-MHC structures.

PANDORA contains useful APIs for pre-processing pMHC template data, identify the most adequate template and adapt the modelling to the specifc case.

Disclaimer: While PANDORA pMHC-I manuscript has been published Frontiers in Immunology , PANDORA pMHC-II paper is under preparation.

Pandora highlights:

• Automated Database collection from IMGT/3d-structureDB

• Modularized peptide:MHC I and II modelling approach

• Flexible modelling scripts (editable by MODELLER expert users)

Tutorial

• Tutorial
  • Download Template Database
  • p:MHC-I base example
  • Run PANDORA on multiple cases (running in parallel on multiple cores)
  • p:MHC-II base example
  • High accuracy modelling (advised to set prepare models for MD)
  • Fast and light modelling
• Advanced Tutorial
  • Multiple levels of parallelization
  • Benchmark PANDORA on one p:MHC-I case
  • p:MHC-I complex with an alpha helix in the peptide

API Reference

• API Reference
  • Database Generation
  • Target Generation
  • Main Module (Pandora)
  • Wrapper Module
  • Contacts Module

Indices

• Index

• Module Index

• Search Page