I am trying to model a protein of length 438aa. It has ~88% identity and ~80% query coverage with existing PDB structures. I had initially used template based modelling using PHYRE2 and SWISS-MODEL. Both of them could not model between residues 1 - 68. The generated model was good. I then went to model via ITASSER. Even here the part 1-68 though modelled but as coils and exists as outliers in Ramachandran plot. The rest of the portion is almost same to the models generated by PHYRE2 and SWISS-MODEL.
- Please advice on how to proceed for MDS and Docking.
- Should I consider the portion that has been modelled correctly only?