[BiO BB] Hydrophobic Core recognition

[Jan Torleif Pedersen]

Dear Iddo,

Not a trivial question !

Use the Protein tools from Stepen Bryant at the NCBI. There is a core
recognition built into their threading program. It may be in the
ncbi-toolkit that you can download from ftp://ftp.ncbi.nlm.nih.gov - If
not I recommend you send an email to Steve directly at NCBI - Hi core
definition program is probably the best one around.

Alternatively use DSSP from embl and select all residues which have low
solvent accesibility. That gives you a pretty good core - but be aware !
If you have large cavities (which you have in most proteins) you will
get a strange definition of the core.

			Regards

				-- Jan




Iddo Friedberg wrote:
> 
> Hi all,
> 
> Does anybody know of a program which, given a PDB (or DSSP or somesuch)
> file can recognize the hydrophobic core?
> 
> Thanks,
> 
> Iddo
> 
> --
> 
> Iddo Friedberg                                  | Tel: +972-2-6757374
> Dept. of Molecular Genetics and Biotechnology   | Fax: +972-2-6757308
> The Hebrew University - Hadassah Medical School | email: idoerg at cc.huji.ac.il
> POB 12272, Jerusalem 91120                      |
> Israel                                          |
> http://bioinfo.md.huji.ac.il/marg/people-home/iddo/
> 
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-- 
Dr. Jan Torleif Pedersen 
Dep. Computational Chemistry 
H. Lundbeck A/S 
Ottiliavej 9 
DK-2000 Valby - Copenhagen 
DENMARK 

phone : +45 36 44 24 25 ext 2887 
FAX : +45 36 30 13 85 
email : jatp at lundbeck.com