Hello Desmond,
I'm assuming by "bindings" you mean protein-protein interfaces? (or maybe
protein-ligand interfaces).
The conventional way is to use multiple sequence aligments and find closely
related proteins. These will usually have similar binding. This is by far
the easiest method. If you do this, it's very unlikely you'll need the CDK.
If you mean to find structurally similar binding sites, you'll need the
Protein Data Bank (PDB) experimental structures, but I'm not aware of any
pre-built tools to find similar shapes. 3D shape matching is still very hard
for computers, so this is usually only done for proteins with high sequence
similarity. Other than that, I can't really help you as 3D shape algorithms
are way outside of my field.
The CDK can help in this approach as general tool, but there is no
functionality that will search for protein similarity. The structure
similarity tools in the CDK are designed for 'small', 'chemical' molecules
like medicines etc., not for insanely huge (bio)polymers.
Hope this helps!
~Jules Kerssemakers
PhD student Bioinformatics,
CMBI, Netherlands
Vriend group
On 22 March 2011 14:20, Desmond Lim <limwen...@gmail.com> wrote:
> Hi,
>
> I'm a new user of CDK (just started) and my boss needs me to proteins
> with similar bindings to one that we have. I have gone through the CDK
> website and can't find any documentation on how to go about doing this.
>
> I'm using Bioclipse. Can someone point me to the right place to start my
> search, an SDK, manual, codes, anything?
>
> Thanks.
>
> Desmond
>
>
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