Automation of loop refinement by MODELER on multiple PDB files with the loop information stored in each file name. (the sample protocol and PDB/loop list file are attached).

This protocol will generate multiple loop models for each PDB file (from the PDB/Loop list) using SA and DOPE methods. Only the best loop based on the user specified score (PDF or DOPE) will be saved into Output.

The following format is used for each PDB file. {PDB ID (or name)}_{Chain Name}{Starting Residue ID}_{Chain Name}{Ending Residue ID}.pdb.

For example,
1ACC_648_651.pdb
1bvn_P215_P225.pdb
1J96_B10_B15.pdb
......

[NOTE]: The current protocol sample can not specify S-S bridge.

Thanks, Hongwei