Question: Maestro (Schrodinger Software), Protein Data Bank,
0
gravatar for Holmes
2.8 years ago by
Holmes0
Holmes0 wrote:

Hi all,

I am new to Maestro and have not done structural biology in quite a bit. I am examining protein structures and trying to find ways to determine properties of proteins I look at from PBD (protein data bank).  Please let me know if this topic is not covered in this forum and if there is a better place to post these questions!  I also apologize in advance for the many questions, I am very curious :)

I am particularly interested in:

  • If I search for a specific protein in PDB, how do I determine how many structures of that protein exist?  Are the multiple structures different confirmations of the same (or similar) AA peptide chains with different or similar biological functions?

  • How do I determine the unique bound ligands there are for a protein? Do I just look through all the different entries and count all the different bound proteins to the structures? It seems that ligands are only attached to proteins and each PBD ID contains a protein and potentially a ligand for that protein.

  • What is the best way to determine the binding site residues in Maestro? Are the green structures within the proteins the different binding sites? Are there ways to look at the amino acid makeup of different binding site residues (e.g. the 2D ligand interaction diagram) for one protein? I seem to be able to only look at one 2D interaction diagram!

  • How does one interpret the 2D ligand interaction diagram? I can't tell what the ligand and what the binding site is (perhaps this is just me being stupid but I want to know!)

Best best best and much love for any answers to the above.

ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 2.8 years ago by Holmes0
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