Subject: SUMMARY: Identifying water in proteins

From: Iraj Daizadeh <[email-masked]>
Date: Fri, 4 Feb 2000 11:43:49 -0500 (EST)

Here's the summary collected from responses to my query concerning the
identification of water molecules within a protein from the CCL
([email-masked]) and the PDB ([email-masked]) mailing lists. 

Programs listed below: GRID, webmol, DOWSER, CNS

Thanks to all participants as well as interested parties.

Iraj.

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QUESTION:
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Are there any programs that identify water molecules within a protein
(from crystallographic data)? We have a one paper which referenced the
GRIN/GRID program from Molecular Discovery Ltd., UK....any information
would on this or other programs would be appreciated....

Will summarize as typical....iraj

Iraj Daizadeh, Ph.D.
Harvard University
Department of Cellular and Molecular Biology
The Biological Laboratories
16 Divinity Avenue
Cambridge, MA 02138
Phone:   (617) 495-0783
         (617) 495-0560
Fax:     (617) 496-4313
Email:   [email-masked]
WebPage: http://mcb.harvard.edu/gilbert/daizadeh
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Dear Dr.  Daizadeh ,
**GRID is a powerful tool for research on biological target. I use it in my
computational studies also to complement 3D QSAR techniques applied to drug
design. It was created from a high merit Scientist , Peter Goodford (Oxford
University) who is my  my personal friend . He recently spent a week in my
department as visiting Professor. GRID is free for the Academy. Contact
Peter at: [email-masked]
Best Regards,
Salvatore Guccione

Salvatore Guccione, Ph.D.
Associate Editor of the European Journal of Medicinal Chemistry
University of Catania,
-Faculty of  Pharmacy-
Dipartimento di Scienze Farmaceutiche,
viale Andrea Doria, 6, Ed. 12 Città Universitaria
I-95125 Catania (ITALY)
Telephone: +39 095 738-4020
Fax:+39 095 504572
email: [email-masked]

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From: G M <[email-masked]>
To: [email-masked]
Subject: Searching for waters

To Iraj Daizadeh,

We do have a program which will identify water molecules inside of
proteins.  Our program is called DOWSER and Helmut Grubmuller in Germany
has a program called SOLVENT.  I have not used his program so I am not
aware of its full functionality.  However, I am very familiar with
Dowser.  If you would like, I will send you a .tar file with the full
src/executable or you can try and log into a development site at NCSA
where I am adding the browser-based version ( it is still in trial mode
but should be working ).  ( M.L. CONNOLLY, "solvent-accessible surfaces
of proteins and nucleic acids", Science, Vol. 221, 709-713 (1983).

here is URL for development version of the Biology Workbench.  You will
have to register to try Dowser.

http://glycine.ncsa.uiuc.edu/structure.html

Geoff Mann

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You'll probabvly get this answer more often: checkout dowser from Jan
Hermans group at UNC chapel hill.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel         Biomedical center, Dept. of Biochemistry
s-mail: Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: [email-masked]    www: http://zorn.bmc.uu.se/~spoel
phone:  46 18 471 4205          fax: 46 18 511 755
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

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Try WebMol at EMBL. I think it shows cavities and water molecules in the
protein.

Bahram Goliaei <[email-masked]>

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Hi,

CNS has a routine to automatically pick water molecules in an X-ray map.
Another option is the program watpeak in the CCP4 suite. In both cases, it
is a good idea to manually check the peaks output by these programs.

Hope this helps, regards

Luca

-------------------------------------------------------------------------------- 
 Luca Jovine
 Structural Studies Division, MRC Laboratory of Molecular Biology
 Hills Road, Cambridge CB2 2QH, ENGLAND.
 Voice: +44.1223.402443. FAX: +44.1223.213556. Telex: 81532.
 E-Mail: [email-masked]
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Iraj,

You might find further information here:

Goodford's grid
    Henrietta Elton
    Molecular Discovery Limited
    West Way House, Elms Parade
    Oxford OX2 9LL
    ENGLAND
    Phone +44-993-830385
    Fax +44-993-830966

My understanding is that GRID will give you potential favorable water
sites in the absence of xray data. Given xray data it's rather straight
forward to look at peaks that have high enough sigma value and are at
proper distances and orientations to potential donors or acceptors.
A number of software packages can be used in concert to 'pick'
electron density peaks and score them as suitable water or possible
solvent ions.

http://xray.bmc.uu.se/usf/
http://www.dl.ac.uk/CCP/CCP4/
http://xplor.csb.yale.edu/cns_solve/

Hth.

Mike
Michael Merckel <[email-masked]>

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From: [email-masked]
To: [email-masked]

There are two different things:

1) Analysing where waters sit in macromolecules, or, if there
   are no waters in the PDB file, finding the cavities that are
   large enough to hold a water.
   Most of the better molecular modelling programs can do those
   things.
   Lets call this ANALYSIS in the rest of this discussion.
2) Predicting where waters would be likely to sit, i.e. calculate
   positions where the potential for water is favourable. Not all
   programs can do that. GRID, as suggested in the original question
   that triggered this discussion, is one of the better programs
   for this type of work.
   Lets call this PREDICTION in the rest of this discussion.

Gert Vriend

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