Subject: Summary-Compressed PDB Lists.

From: "NOYM" <[email-masked]>
Date: Wed, 8 Nov 1995 13:53:08 +0100

Dear Colleagues,

Thank you all for the replies to my question about a compressed
pdb-list. They have been very useful for me.

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 The PDB directory currently consists of about 3800 records. However,
 many of these are different versions of the same structures (for example different 
mutants of the same protein or one protein with a 
number of different ligands or a lot of DNA/RNA structures).

 It would, for a number of reasons, be very valuable to have a subset of the PDB 
containing representatives ("the best structure") of each unique protein, and important 
conformers. If anybody have done a comprehensive investigation to compile such a list
or if it is already available on the net please let me now !  I'm also 
interrested in any hints how to do this without manually going through 
every record in the PDB. 
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Here follows a summary:

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CATH:

You can also get similar information from our CATH web page, where
Chris Orengo and Alex Michie have developed a hierarchical numbering 
system for related folds and sequences.  I suggest starting with 
http://www.biochem.ucl.ac.uk/bsm/biocomp/index.html
										rob.
                    ----|------

My comment: Take a look at this site if your into bioinformatics !
it contains structural classifications of proteins ( like in SCOP),
algorithms for threading etc.

                    ----|------ 
My comment again: Take also a look at the SCOP database (http://
scop.mrc-lmb.cam.ac.uk/scop/) !

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PDB_SELECT lists from the EMBL:

Hi, It's been done by many people. Perhaps best by Sander's group at
 EMBL. You can get their latest PDB_SELECT lists from the EMBL file
 server (ftp.embl-heidelberg.de). A reference describing their method
 is Protein Science, 1, 409 ' 92.

          Hope this helps (or keeps you from redoing it yourself!),
               Jay Ponder, Washington Univ, St. Louis

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DALI: Comparison of protein structures in 3D:

I believe Chris Sander at EMBL has already done similar work (Hobohm & 
Sander, Protein Sci., 1994, 3:522-544) which should be accessible via the 
Net/Web at http://www.sander.embl-heidelberg.de.

Good luck,

Scott
				----|------

My comment:

This site should also be checked if your into bioinformatics:

Below is a text I've extracted from the DALI web site
(http://www.sander.embl-heidelberg.de). Here you also find
a map of proein structure relations in a clustering diagram
(look at the FSSP database):

"The Dali server
 
The Dali server is a network service for comparing protein structures in 3D. You submit 
the
coordinates of a query protein structure and Dali compares them against those in the 
Protein Data
Bank. A multiple alignment of structural neighbours is mailed back to you. In 
favourable cases,
comparing 3D structures may reveal biologically interesting similarities that are not 
detectable by
comparing sequences. If you want to know the structural neighbours of a protein already 
in the
Protein Data Bank, you can find them in the FSSP database. 
You can ... 

     submit coordinates by email (recommended) 
     submit coordinates interactively (experimental) 
     read a paper about the Dali method 
     read a review about structure searches 
     send feedback to the Dali authors 
     get help with the Dali server 
     retrieve precalculated structural similarities from the FSSP database 
     look at 3D views of examples of unexpected structural similarities 
     look at statistics about WEB access to Dali "

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General comment:

Comment from Max Vasquez,

Several such compilations have been published by Chris Sander's group at
the EMBL-Heidelberg (check their web site for an updated list) as well as
by others (I happen to have a reference by Orengo and co-workers in Protein
Engineering 6, 485 [1993]).  Just be aware that these compilations tend to
be more compressed that one may bargain for.  For example, just one or very
few serine proteases are included, similarly for immunoglobulins, etc.

Best wishes,

Max Vasquez, PhD,  <[email-masked]>

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Laura Walsh Annotated PDB File Listing:

	Suggested citations for use of this file are:
   L. L. Walsh, "Annotated PDB File Listing", Protein Science 1:5,
                 Diskette Appendix (1992).

She has broken down the PDB by molecule or compound.
The latest revision I have of the listing is April 1994.  Does anyone
know of a more up to date listing?
 
                                                Jeff Nauss
                     ----|------

My comment: Yes, the most updated list may be found in Lauras reply
below. This list is very useful even now in the web-era. It contains
a list of each molecule in alphabetic order with the resolution 
and other important information of each record in the PDB. The only
drawback is that I have not found any more recent updates than from
the Jan 94 release (see below for info of this release):

                     ----|------

I did this a year ago last August.  The results can be obtained from my 
www site:

http://www.scs.uiuc.edu/~lwalsh

A citation for a paper published about the process is included in the 
Work in Progress Annotation.

Laura Walsh, <[email-masked]>

                    ----|------

Also available at:

Did you have a look at files in CCL archives in:
/pub/chemistry/documents/PDB/PDB_file_list
on www.ccl.net ?

Jan
[email-masked]

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Commercial:

 ...It is also only part of the story, in that there are
also inconsistent atom labeling, so that searches for a given structure
won't always find all of those hits.  I don't know what public domain fixes
there are, but I do know that Oxford Molecular went through the PDB
database, making it consistent and fixing up irregularities.  They now offer
it as relational database called Iditis, so you should try contacting them. 
Their web page is at:

 http://www.oxmol.co.uk/

or I you could send email to:

 [email-masked]

Good luck,

Ernest Chamot, <[email-masked]>

				----|------

Comment from Pieter Stouten:

I always wondered why they would use a relational database paradigm.
Proteins are ordered and the information one wants to retrieve often
involves stretches of residues with certain characteristics. Using a
relational database, one needs to do many operations. It seems to me that a
mixture of pattern matching (with additional bonus of easily allowing for a
few mismatches) and relational operations would be much more efficient.
Does anybody have any opinions about this?

Thanks, 
Pieter Stouten  <[email-masked]> .

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Martin Norin, Ph.D.		e-mail:[email-masked]
Dept. Struct. Biochem.
Pharmacia Biopharmaceuticals
Stockholm
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