Re: Can "PDB" license be considered free ?
On Mon, 07 Mar 2016, Peter Rice wrote:
> We had this discussion some years back about SwissProt protein
> sequence entries included as test data in EMBOSS. We also have PDB
> files in the EMBOSS test data.
>
> The conclusion was that scientific data (SwissProt, PDB, etc.) are
> scientific facts and it is not reasonable to require permission to
> change them.
This isn't true; there are loads of reasons to change sequences and
structural models of proteins. Protein sequences are just based on
references which have inaccuracies and do not represent ancestral
sequences or the true variation present in real populations; in my lab
we modify UniProt sequences and redistribute those modifications in
publications all of the time.
PDB files are also just the current model of a particular
crystallization of a particular set of molecules. It's pretty standard
practice to modify them using simulations to account for different
binding partners and assemblies. [I've published the PDB files
containing these modifications, for example.]
All of that said, because PDB and UniProt files are not works of
authorship, they likely do not qualify for copyright protection in the
US, so the licensing terms can largely be ignored. However, that may not
be true of other jurisdictions.
--
Don Armstrong http://www.donarmstrong.com
It is easier to build strong children than to repair broken men.
-- Frederick Douglass
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