sha256feng / model-long-missing-loop

This repository contains code and examples to model multiple missing loops in tetrameric protein.

Model-long-missing-loop

This repository contains code and examples to model multiple missing loops in tetrameric protein.

Modeller script is mainly based on following link: https://salilab.org/modeller/wiki/Missing%20residues

Original resid	Afterwards	Original resid	Afterwards
561	561-74=487	589	589-74=515
416	416-74=342	427	427-74=353
693	693-74=618	698	698-74=624

../../bin/mod9.21 mod-seg.py to execute the python script for Modeller. mod9.21 is an executable version of Python and Modeller.

- Execute the loop modeling for each chain. Mutate the "A" letters in `two-alignment.ali` to "B"/"C"/"D" letters. And run them in separate folder, because the output PDB files have the same names. Later I visually checked each chain's modeling result and `cat` them together.
List of output files as example:


- Loop modeling results: loops forming a knot -- need to fix 

Two segments have knotted structure of peptides. In order to prepare a cleaner version where there is no such problem, I use CHARMM script to solve this bad penetration issues. The program requires feeding of PSF and CRD files. So I generated PSF and CRD file firstly by CHARMM-GUI's PDBReader. Later I used following script to rotate the loops and did some minimization to avoid clash and bad angles.

Solve ring penetration issue

Read input structures:
   - step1_pdbreader.psf
   - step1_pdbreader.crd

Processing CHARMM script:
   - step2_pene_solve.inp

Principle:

• Set some parts movable and others fixed;
• Rotate, translate the movable part;
• Local minimization first, then global minimization;