Flexible Residues

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Flexible Residues

Postby mwells » Fri Nov 20, 2015 1:35 am

Hello Sargis,

I have a question regarding screening flexible residues. When you create the flexible residue structure a flex file and a rigid file are saved under a flex subfolder (i.e. macrolecule/Target_flex).

To screen the flex model I read you simply select the Target_flex subfolder. The flex subfolder contains both flex and rigid structures. However when I do this I only get the rigid structure appearing and PyRx states it is binding only to the rigid structure. Is this correct?

Cheers,

Mike
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Re: Flexible Residues

Postby sargis » Fri Nov 20, 2015 4:08 am

Hello Mike,

That is correct, when you create the flexible residue structure a flex file and a rigid file are saved under a flex subfolder. When you go through the Wizard (AutoDock or Vina), PyRx would show only the rigid structure. The flexible residues appear when you run the docking and the binding is to both the rigid and flexible part. Both AutoDock and Vina store flexible residues together with the ligand in the output file. When you go through docked conformation, you'll see flexible residues conformation changing together with the ligand.

Hope this make sense.

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Sargis
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Re: Flexible Residues

Postby mwells » Fri Jun 24, 2016 8:24 pm

Hello Sargis,

I hope you are well. I I have a question regarding making a flex structure once again. I am trying to dock to a protein containing a heme group. This heme group is stored as Chain B and the protein sequence in Chain A. When I make residues flexible in the protein chain the heme group no longer appears. Does the program keep the space where the heme should be? How do I bring the heme along in the structure for the docking? Do I somehow need to merge the heme with the protein chain? Any advice would be appreciated.

Cheers,

Mike
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Re: Flexible Residues

Postby sargis » Sat Jun 25, 2016 2:12 am

Hello Mike,

I hope you are well too. Can you please copy pdb id or upload the input file here. I've tried this with a couple of examples from pdb and kept the heme group. You can also make pdbqt without flex structure and then copy the lines corresponding to heme atoms to _rigid._pdbqt with a text editor.

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Sargis
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Re: Flexible Residues

Postby mwells » Sat Jun 25, 2016 2:55 pm

Hi Sargis - problem is the pdb is confidential and not in public domain. I tried adding heme to end of rigid pdbqt via notepad but it didn't seem to work. It opens up in pymol with heme but not in PyRx. Is there a specific location in the description in notepad where you should add heme? If you want to reply directly to my email please let me know.

Mike
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Re: Flexible Residues

Postby sargis » Sun Jun 26, 2016 7:18 pm

Hi Mike,

I've created a new update for PyRx that would keep the heme in the second chain. Please use Help->Check for Updates... menu to apply this update. Complete list of changes for this update is available at https://sourceforge.net/p/pyrx/wiki/Changelog/

I appreciate your feedback on this.
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Re: Flexible Residues

Postby mwells » Sun Jun 26, 2016 10:37 pm

Thank you kindly for all your help Sargis - I will try it out and let you know if there are any issues.
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