In RCSB PDB, I can download much ligand files and use it for docking, but, there is two options to download a ligand: Model and Ideal.
In RCSB PDB site I don't find what is the difference between this 2 formats. I have this examples files:
http://files.rcsb.org/ligands/view/HEM_ideal.sdf
http://files.rcsb.org/ligands/view/HEM_model.sdf
Dear Wandré Nunes de Pinho Veloso,
There is no difference between the two. Ideal and Model can be written in the same format and can be viewed by the same program. In addition, they can be viewed by more than one program.
I tried to view the following (see links below; IDEAL & MODEL) and I succeeded to view them by ArgusLab program:
http://files.rcsb.org/ligands/download/HEM_ideal.pdb
http://files.rcsb.org/ligands/download/HEM_model.pdb
You can view other links by different programs, for example:
http://files.rcsb.org/ligands/download/HEM_ideal.sdf
http://files.rcsb.org/ligands/download/HEM_model.sdf
For more, please see the following link:
http://www.rcsb.org/pdb/static.do?p=download/http/index.html
Hoping this will be helpful,
Rafik
ya.. a small difference is there. you can get the idea from following link
http://wwpdb.org/data/ccd
Dear Rafik,
I see some differences between the files, but, not in format. I wan't know what the differences or why one is called IDEAL and another is MODEL. I only see differences in X, Y and Z coordinates. All molecules are the same, verified by the SMILES of them.
As per my understanding, The "model" is coordinates obtained from the experiments. The Ideal is the same experimental coordinates are optimized from the computational methods.
This information is official? I am writing about this in my thesis, so, I have to be sure about this...
I can't find anything about the differences...
In a research article of John Westbrook stated that "A set of model coordinates from a single experimental entry and a computed set of ideal coordinates are provided".
please find the quote from the reference: Bioinformatics. 2015, 31(8):1274-8.
Dear Wandré Nunes de Pinho Veloso,
Model (X-ray structure 1IEP) and Ideal (energy minimized) coordinate sets:
Please see the following link:
http://prody.csb.pitt.edu/manual/reference/proteins/pdbligands.html
Hoping this will be helpful,
Rafik
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