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Protein-Ligand in PDB

In some protein crystallography studies, the protein crystals are grown with the substrate/ligand/inhibitor added, thus the resulting structure contains both the ligand and the protein atom ...
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What is the different between the I-TASSER, phyre2, SWISS-model in the 3D tertiary structure?

This is a common Q. Briefly, you have some techniques here that get used separately or combined: Ab initio: assemble the protein from scratch, often via a library fragmented peptides (3-mer, 6-mers, ...
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