modelWrap

wrapper for automatized homology modeling of multiple number of sequences on one template structure using "modeller_9.x"

Important

• the script only works with a template given, therefore only the structural alignment and the model building are implemented.
• no model evaluation is implemented!

Workflow

• Given .fasta file (including all sequences to process) is seperated in single files
• .fasta files are converted into the structural file format .ali
• align2d.py files are generated for each sequence
• align2d.py files are processed by modeller -> alignment files are written
• automodel.py files are generated for each sequence
• homology models are generated by modeller
• everything is cleaned up and .pdb files are stored in the directory

Requirements

• modeller_9.x
• python3 (modeller is also executable without installed python3, however this has to be changed in the script (python3 <-> mod9.x))

Installation

Bash script, just make it executable and run

SourceCode compiling with Argbash - argument parser generator

template file can be changed and converted to executable code (tested with argbash_2.8.1; Ubuntu_16.04)

argbash modelWrap_template -o modelWrap