Generating Conformers of Folded Proteins

[RC-2000]

Hello,

Thanks for creating this software. We're interest in generating conformers from a directory of folded proteins. How can we do this?

[joaomcteixeira]

Hi @RC-2000 Thanks for your question. Here we go :wink:

In the example/ folder, there is a mini-tutorial on generating conformers for a small peptide. But those are general guidelines that apply to any protein.

To generate conformers from your set of folded proteins, you must create the "torsion database" (as we call it) from those proteins. For that, skip this initial line in the mini-tutorial because you don't need to download the PDBs. :point_down: :

idpconfgen pdbdl cull100 -u -n 2 -d pdbs.tar

Instead, create a .tar file from your PDBs. For example:

cd folder_with_my_pdbs
tar -cf pdbs.tar *.pdb

Afterward, continue following the steps in the mini-tutorial. In summary, you need to do all steps except for the one of downloading the PDBs, which you replace by providing the sscalc command your pdbs.tar file. Everything else is the same.

Please let us know if you have any other questions. We are very pleased you're using IDPConfGen.

Cheers,

[menoliu]

Hi @RC-2000, thanks for reaching out! If your question pertains to generating intrinsically disordered tails on PDB structures of folded domains, we have an experimental feature in my branch on PR #231. There is documentation within that branch as well on how to use the fldrs sub-client.

Please don't hesitate if you have any further questions/suggestions.