[Chimera-users] Fitting ligands/substrates to protein structure

Jason Jeffrey Rodencal rodencal at stanford.edu
Thu Dec 5 12:28:04 PST 2019

Hello chimera users!

I've been browsing the various tutorials for chimera and I've seen a lot of amazing models of proteins bound to DNA, ligands, etc. I have a pdb file for my protein of interest and its substrate, and I have the active site of the protein. I was wondering if there's any way of predicting how the substrate fits into the catalytic cleft. Is there some easy code or application that can do this in chimera or is this a far more challenging task than I appreciate?

Thank you!
Jason Rodencal
Dixon Lab
Stanford University

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