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Homology Models

Building models using modeller 9.23 and a single template and scripts to generate models using single and multiple templates

IMPORTANT Before running, please change the Path in making_models_single.py and making_models_mult_templates.py to location where templates and models must be saved in

To run using single template

python3 making_models_single.py 3qh7_A.pdb T1001.ali

To run using multiple templates

python making_models_mult_templates.py T1001 list_templates.txt

Saves the outputs and models in T1001-models and T1001-mult-models for single and multiple template prediction respectively

To convert fasta to ali, use convert_fileformat_modeller.py, NOTE: there are other useful scripts in the scripts folder

  • For running PSI-BLAST and downloading associated PDB structures: run_psiblast.py and download_pdb_blastoutput.py
  • For running HHsearch and downloading associated PDB structures: run_hhsearch.py and download_pdb_hhroutput.py
  • To read the outputs and download PDBs from the search outputs: combined_blast_hhr_templates.py and download_templates.py
  • For calculation of RMSD among the predictions and performing clustering: calculate_rmsd.py, calculate_rmsd_biopython.py, AMC.py, HCS.py