Hello Desmond,
The links Egon suggests are worthwhile reading, so you should definitely
check them out.
As for your method: how do you plan "to find a protein that can bind to that
[ligand]"? The search for similar proteins given a known sequence is a
solved problem (see: BLAST), but seeing if a ligand fits a molecule is not a
solved problem.
It's not a problem if your ligand is already in the PDB, but if you have a
new ligand, the search will be way more difficult, because you have to dock
your ligand against all PDB structures to see if if fits. Docking is a LOT
of work, often taking half an hour to a few hours per ligand-structure
combination, so doing this for 1000's of structures...
You could optimise this a bit by filtering your structure list. E.G. by only
testing protein structures that are very different from all others (e.g.
<90% sequence identity), and by filtering structures that already have
ligands that look very much like your own ligand (ligand structure
similarity: e.g. Tanimoto Coefficient, or others). Maybe you have other
information, like what sequence-domains bind your ligand, etc. That could
also help a lot.
I may also completely miss another approach, because I am very much
structure-minded (both chemically speaking and protein wise). You may be
able to find something by sequence, but I wouldn't know how from the
information you have given us.
Good luck!
~Jules
On 23 March 2011 08:42, Egon Willighagen <egon.willigha...@gmail.com> wrote:
> On Wed, Mar 23, 2011 at 8:29 AM, Desmond Lim <limwen...@gmail.com> wrote:
> > Can you point me to places where I can find either examples or API?
>
> I have been writing up an introduction to the CDK API as a book. The
> first edition is out a couple of weeks now:
>
> http://chem-bla-ics.blogspot.com/2011/02/groovy-cheminformatics.html
>
> The full JavaDoc is available at:
> http://pele.farmbio.uu.se/nightly-1.4.x/cdk-javadoc-1.3.8/index.html
>
> (Update the version number for 1.3.8 when later versions are out...
> or, just visit the nightly build service:
> http://pele.farmbio.uu.se/supernightly/ and look out for the 'Browse
> online' links for the API Documentation)
>
> Obviously, you should have a look at least at these classes:
>
> - org.openscience.cdk.io.PDBReader
> - org.openscience.cdk.geometry.alignment.KabschAlignment
>
> I hope this helps,
>
> Egon
>
> --
> Dr E.L. Willighagen
> Postdoctoral Researcher
> Institutet för miljömedicin
> Karolinska Institutet
> Homepage: http://egonw.github.com/
> LinkedIn: http://se.linkedin.com/in/egonw
> Blog: http://chem-bla-ics.blogspot.com/
> PubList: http://www.citeulike.org/user/egonw/tag/papers
>
>
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