u/arielabom

Hi everyone,

I’m working with a recombinant Fab antibody and I’m trying to model its PEGylation, specifically the covalent attachment of a PEG (around 40 kDa) via a maleimide group to a cysteine residue.

I already have predicted structures of my Fab, but I’m unsure about the best approach to model the PEG conjugation and visualize where/how the PEG chain would be attached.

My main questions are:

What software would you recommend for modeling covalent attachment of PEG to a protein (especially via cysteine–maleimide chemistry)?

Are there any tools that can handle flexible polymers like PEG reasonably well?

Would docking tools (e.g., AutoDock) be appropriate here, or is molecular dynamics a better approach?

Are there any good papers or reviews on computational modeling of PEGylated proteins?

Any suggestions, workflows, or references would be greatly appreciated!

Thanks in advance 🙂

Hi everyone,

I’m working with a recombinant Fab antibody and I’m trying to model its PEGylation, specifically the covalent attachment of a PEG (around 40 kDa) via a maleimide group to a cysteine residue.

I already have predicted structures of my Fab, but I’m unsure about the best approach to model the PEG conjugation and visualize where/how the PEG chain would be attached.

My main questions are:

What software would you recommend for modeling covalent attachment of PEG to a protein (especially via cysteine–maleimide chemistry)?

Are there any tools that can handle flexible polymers like PEG reasonably well?

Would docking tools (e.g., AutoDock) be appropriate here, or is molecular dynamics a better approach?

Are there any good papers or reviews on computational modeling of PEGylated proteins?

Any suggestions, workflows, or references would be greatly appreciated!

Thanks in advance 🙂