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Help about protein database.

Cornelius Krasel zxmkr08 at studserv.zdv.uni-tuebingen.de
Wed Jun 9 05:05:00 EST 1993

In <9306081345.AA12019 at net.bio.net> CZJ at CU.NIH.GOV writes:

>> Date: Mon, 7 Jun 93 19:59:15 CDT
>> From: hhuang at conch.senod.uwf.edu (Hong Huang)
>> Message-Id: <9306080059.AA25947 at conch.senod.uwf.edu>
>> To: bio-soft at net.bio.net
>> Subject: Help about protein database.
>> Hello friends:
>> I'm currently a computer science graduate student and going to have a project
>> forcusing on the 3D structure of protein and the Amino Acid sequence. Would
>> anybody be so kind to tell me about:
>>     (1). the protein structure databases (PIR, PDB, GenBank...) and their
>>          contents (primary, secondary, or ternary structure), and data format.
>>     (2). the existing shareware for modeling the protein 3D structure.
>>     (3). the possibility of predicting the protein 3D structure from amino
>>          acid sequence.
>> or where can I find the answers. Please send any suggestion or answer to:

The only 3D database I know of is the protein data bank (PDB).
All the others archive the primary structure either of
genes (Genbank, EMBL, DDBJ, NBRF come to mind) or proteins
(PIR, Swissprot).

>There are a number of things out there.  The best book for a
>basic understanding of Protein Structure remains the book
>by Dickerson and Geis.  Check your library.  It is about
>20 years old, but the concepts have not changed that much.

For a basic grasp on protein structure, I would recommend
Carl Branden and John Tooze, Introduction to Protein Structure,
Garland Publishing Inc., New York, London 1991. This book
has received very positive critiques in TIBS, July 1992.

>I would also recommend the Protein Society.  They distribute a
>program called kinemage for modeling protein structures and
>the journal contains graphics on a disk.  Membership for
>students is quite reasonable.

Kinemage runs on Macs and PCs (currently) and is also available
by anonymous ftp from the major bio-gopher holes. You cannot
do molecular modelling with it, but it is very nice for
viewing protein structures.

/* Cornelius Krasel, Department of Physiological Chemistry, U Tuebingen    */ 
/* email: krasel at studserv.zdv.uni-tuebingen.de                             */
/* "People are DNA's way of making more DNA." (R. Dawkins / anonymous)     */

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