[BiO BB] Seperation of Protein PDB into multiple units having binding sites

Shameer Khadar skhadar at gmail.com
Mon Sep 25 03:44:09 EDT 2006

To get a hold of all teminology related to subunits and subdomains
Grab the book and Read it once or twice :)
Bioinformatics : Genes, Proteins & Computers
Eds. Christine Orengo and JM Thornton

To split your proteins try with PROTEIN PEELING approach,
Web Server is available here : http://www.ebgm.jussieu.fr/~gelly/

Happy splitting with your proteins,
Shameer Khadar

On 9/23/06, Kalidas Yeturu <ykalidas at gmail.com> wrote:
> Hello Everyone
>  I am working on protein binding sites. I am not yet very much familiar
> with terminology - subunits,domains etc.,
>  My work requires obtaining/splitting a protein PDB into various
> structural units such that each has binding site.
>  For example 1A4G neuraminidase has two structural units - chain A and
> chain B both having binding sites.
>  But splitting a PDB based on chain-id alone, may not always be correct.
> Some manually curated database would be better.
>  I would be grateful if anyone can cite a database where protein-PDB files
> corresponding to structural units having binding sites are provided for each
> protein.
> Thanking You
> --
> Kalidas Y
> http://ssl.serc.iisc.ernet.in/~kalidas<http://ssl.serc.iisc.ernet.in/%7Ekalidas>
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