Re: [ccp4bb] sequence from pdb

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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From: Paul Lindblom lindblom {- dot -} paul {- at -} GOOGLEMAIL {- dot -} COM
Date: 2010-04-06

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Subject: Re: sequence from pdb
From: Miri Hirshberg miri {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2010-04-06

Subject: Re: sequence from pdb
From: Miri Hirshberg miri {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2010-04-06

Mon., April 5th 2010
EBI

several options with no need for extra software:

(1) goto http://www.ebi.ac.uk/pdbe/
left handside under "Get PDB by ID" enter a pdb idcode for example 1mh1
you get
http://www.ebi.ac.uk/pdbe-srv/view/entry/1mh1/summary
goto Structure primary and click Fasta

cut and paste the sequence

(2) pickup the file, it contains all fasta sequences
ftp://ftp.ebi.ac.uk/pub/databases/rcsb/pdb-remediated/derived_data/pdb_seqres.txt

(3) or pickup this file which is a better format of JUST proteins

ftp://ftp.ebi.ac.uk/pub/databases/msd/pdb_aa.fasta
(all peptide sequences in released PDB)

Miri
PDBe EBI

> Is there software that will extract a protein sequence in either 3 letter
> or single letter code from a given pdb file?
>
> Rex Palmer
> Birkbeck College

On Sun, 4 Apr 2010, Rex Palmer wrote:

> Is there software that will extract a protein sequence in either 3 letter or
> single letter code from a given pdb file?
> Â
> Rex Palmer
> Birkbeck College

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Self Rotation function - NCS
From: Paul Lindblom lindblom {- dot -} paul {- at -} GOOGLEMAIL {- dot -} COM
Date: 2010-04-06

Next message:
Subject: Re: sequence from pdb
From: Miri Hirshberg miri {- at -} EBI {- dot -} AC {- dot -} UK
Date: 2010-04-06