This repository contains prerequisite files + more to be used while modelling proteins with Modeller

• pdb2fasta.pl

  • a perl script to obtain a FASTA sequence for a desired protein.
  • usage: perl pdb2fasta.pl protein.pdb

  This FASTA sequence is to be used in the 'structure' part of model.ali whereas the 'sequence' part refers to the full sequence of that protein which can be obtained from Uniprot.

  • This perl script was created by Ranjit Vijayan in March 2006

  (a former member of SBCB, Dept of Biochem, Uni of Oxford, and a Professor in the Dept of Biology, UAE Univ, as of Sep 2023)

• model.ali

  • an example alignment file (model.ali) to be used by Modeller

• model.py

  • an example python script (model.py) to be used to run Modeller
  • usage: mod9.16 model.py # check modeller version

• dope_scores.py + dope_scores_least.sh

  • scripts to be used in conjunction to obtain DOPE scores of all protein models generated and determine the protein model number with least DOPE score
  • Instructions to run are provided at the end of the model.py script