Fix an X-ray diffraction PDB model containing missing residues in complex with native ligand

[fransdany]

Hi,

I’d like to know if there is a feature in D-I-Tasser that can 'repair' an experimental PDB model of X-ray diffraction with missing residues by filling the gaps using a reference protein sequence and reconstructing them while retaining the remaining 3D conformation and interactions with the native ligand. Such PDB models usually don't pose a big problem when we perform molecular docking, but they will when we do MD simulations.

I found a similar question posted in this forum, but it's for the models from Cryo-EM and we can use DEMO-EM for that purpose.

Thank you all in advance.

[XiZhang]

Dear user,

For D-I-TASSER, we don't have user-indicate-template-restraint currently. You could try the I-TASSER server (https://zhanggroup.org/I-TASSER), and then upload your PDB model as restraint from "Option I: Assign additional restraints & templates to guide I-TASSER modeling." -> "Specify template with alignment".

If you have more questions, please feel free to reach out.

Best,
Xi

[rose42snowden]

While D-I-TASSER is primarily a protein structure prediction tool from sequence, and excels at generating full-length models, its core functionality isn't specifically designed for "repairing" existing experimental PDBs by directly filling gaps while strictly maintaining the original 3D conformation and interactions with native ligands. Its strength lies in building models from scratch or using templates, which might lead to changes in the overall structure. For repairing PDB models with missing residues from X-ray diffraction, tools like PDBrestore or MODELLER are more suited, as they can reconstruct missing loops and segments while attempting to preserve the surrounding native structure and interactions, which is crucial for subsequent MD simulations paybyplatema login page

[fransdany]

Noted. Thank you all for the reply

Best,
Frans