Dear All,
My initial or original predicted model of protein has all the amino acid sequences in the polypeptide chain. But when I docked this structure with its partner protein, the resultant model has some residues missing the structure file. Because of this, the alpha helices are broken when visualized in Chimera and Pymol. I carefully checked and the few residues were missing and if some are there but were not forming the bond linkage with the subsequent residues.
I tried building those residues in chimera and have not remodeled using swiss PDB as I do not want to disturb the present docked conformation. Rather, I would like to build those missing links in the same docked structure. Is there any way I can do it ? The Chimera didn't work and giving the error message (Also, I didn't see any options for the reference sequence to upload so that it would build them based on the provided a.a sequence).
Hi Prem I would recommend to MODELLER Missing Residue Model while restraining the already present residues, see link below:
https://salilab.org/modeller/wiki/Missing_residues
Its really easy although you would have to download MODELLER;
if you decide to go this route feel free to ask me any questions
aside from downloading MODELLER. I just executed this command
and my resulting protein exhibited a zero RMSD.
Best,
Joel 💡
Is it possible that the "missing" residues are non-standard amino acids (e.g. post-translational modifications)? Look at the areas in question in the original pdb file in an all-atom representation, e.g. stick representation
Annemarie Honegger Dear Dr. Honegger, that could be the possibility. However, I have modelled this structure using alphafold (through EMBL Database gateway). And I checked the PDB file there are no non-standards amino acids residue in it. The missing residues are only found after docking the model with it's potential protein partner. Because it doesn't look good and information about those residue may be important so I want to build those missing residues without disturbing the restraints after docking, as the docking results are very promising.
Annemarie Honegger Yes Dr. Honegger ! Can I have your email ID so that I can send you through that ? I highly appreciate it.
Best regards
Prem
You can use the "send message" function on research gate to send a private message.
Prem Prakash : Looking at the files you sent me, I could not find any unusual features in your starting model which could explain the problem.
In contrast, the result file not only misses a few amino acid residues, but also contains multiple instances of other residues in different locations (see attached image)
How did you extract the ligand pdb from the docked complex?
Many docking programs return multiple solutions (poses) generated by the docking process in a single pdb file, separated by MODEL/ENDMDL records. Viewer programs by default show only MODEL 1, but offer options to toggle through the additional poses. In Chimera, you would use the MODEL panel to do this.
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/modelpanel.html , https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html
The result file you sent me could have been generated by extracting a single docked pose in a way that did not properly isolate one specific pose, but took along a few residues from other poses and lost a few residues from the intended pose.
Annemarie Honegger Dr. Honegger, Thanks you so very much for your support. I had downloaded the PDB files just from the output of docking program. I have no clue how those residues are broken and scattered like that.
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