Question: How to prepare Protein-Ligand complexes for MachineLearning
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gravatar for fabio.oliveira
7 weeks ago by
fabio.oliveira20 wrote:

Hello! I am trying to construct a new data set of protein-ligand complexes labeled with affinity data. The plan is to extract features from the protein-ligand complex. But to do that I need to clean the complex structure.

I wonder what are the community favorite pipelines and open source programs to prepare/clean pdb files?

Cleaning / preparing the pdb file can mean that I need to do the following: Add missing heavy atoms / hydrogen atoms. Build missing loops. Convert non-standard residues to their standard equivalents. Select a single position for atoms with multiple alternate positions listed. Delete unwanted chains from the model. Delete unwanted heterogens.

Looking forward to read about your approaches!

ADD COMMENTlink modified 22 days ago by Biostar ♦♦ 20 • written 7 weeks ago by fabio.oliveira20
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