[Biopython] Mining the PDB header

[Lenna Peterson]

I am not aware of any formal information about either function or
localization within PDB files.

On Thu, May 11, 2017 at 3:55 PM, Ahmad Abdelzaher <underoath006 at gmail.com>
wrote:

> Sorry for the misunderstanding, but I'm mining the structures
> themselves. To be more precise, I'm doing structure prediction
> analysis. I'm not doing text mining of the headers themselves. I'm not
> sure which classification is used in the PDB, how consistent it
> is,...etc. I would be interested in any information regarding the
> function, or localization,..etc. If you think I'm not quite sure what
> I want, you'd be correct. Ultimately I will be clustering the
> structures based on that classification.
>
> On Thu, May 11, 2017 at 8:28 PM, Lenna Peterson
> <lenna.peterson at gmail.com> wrote:
> > Well, your original question did ask how to mine the PDB header with
> Python.
> >
> > "protein classification" is not a specific term (do you mean organism?
> > function? fold? etc.) - is this something that appears in the PDB
> header? If
> > so, what PDB header field is it in?
> >
> > Lenna
> >
> >
> > On Thu, May 11, 2017 at 1:49 PM, Ahmad Abdelzaher <
> underoath006 at gmail.com>
> > wrote:
> >>
> >> I'm not trying to mine the actual header. I would definitely be
> >> interested in an option that retrieves the protein classification
> >> without having to write any additional code. Does such option exist?
> >>
> >> Regards.
> >>
> >> On Thu, May 11, 2017 at 7:06 AM, João Rodrigues
> >> <j.p.g.l.m.rodrigues at gmail.com> wrote:
> >> > You can do *some* mining. Look at parse_pdb_header.
> >> >
> >> > 2017-05-10 18:58 GMT-07:00 Ahmad Abdelzaher <underoath006 at gmail.com>:
> >> >>
> >> >> Hey guys,
> >> >>
> >> >> Unfortunately  I read this in the FAQ page:
> >> >>
> >> >> " If you are interested in data mining the PDB header, you might want
> >> >> to look elsewhere because there is only limited support for this."
> >> >>
> >> >> So if I can't do it with biopython, what other alternatives do I
> have?
> >> >> I'm doing some PDB mining and I'm interested to retrieve the
> >> >> classification of the structure, to do some clustering analysis
> later.
> >> >>
> >> >> Cheers.
> >> >> _______________________________________________
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> >> >
> >> >
> >>
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> >
> >
>
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