RosettaAntibody, Fv without terminal 3 residues

[Anonymous]

Hi Everyone. I have a question for RosettaAntibody in local machine.

I installed Rosetta++ in my local machine, and downloaded all database related NCBI. and then I have tried to made Fv homology modeling by RosettaAntibody in my local machine.

Just after executing bash, which was generated in build folder, I confirmed the strucure PDB files. They all defects 3 amino acid residues in both (N- C-) terminal region. But in RosettaAntibody Server, the final output candidate structures have all amino acid reisudes.

Is it ordinary phenomenon? or I didn’t add any particular options for modeling all residues at runninng rosetta++?

Best Regards,
yuich

[Anonymous]

Dear Yuich,

The RosettaAntibody server has an updated antibody database compared to the release version of RosettaAntibody. Thus it is probably that the web server selected a template that was not available in the original RosettaAntibody release. From a practical standpoint, the last three residues are not very relevant for antibody-antigen interactions (in most cases). Furthermore in cases that the three residues are present the quality is not good, and in most scenarios the crystallographer simply put them in there, so the positions might not be accurate. In such cases the coordinates could be misleading. Thus if I were you, I would not read too much into those terminal residues.

Trust this helps,
Aroop

[Author]

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