[BiO BB] Hydrophobic Core recognition
Jan Torleif Pedersen
jatp at lundbeck.com
Tue Aug 28 12:15:59 EDT 2001
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.
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?
> 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 |
> BiO_Bulletin_Board maillist - BiO_Bulletin_Board at bioinformatics.org
Dr. Jan Torleif Pedersen
Dep. Computational Chemistry
H. Lundbeck A/S
DK-2000 Valby - Copenhagen
phone : +45 36 44 24 25 ext 2887
FAX : +45 36 30 13 85
email : jatp at lundbeck.com
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