[Molvis-list] adding hydrogens to a pdb file

[Ilan Samish]

We did an extensive check on the accuracy of adding hydrogens. Seems that
the best software is the one by the Richardson group called REDUCE
(downloadable). See web interface within the molprobity online package:
http://kinemage.biochem.duke.edu/molprobity/index-king.html

We are currently collaborating with the Richardson lab in developing an
easier web interface / "PDB-with-H database" solely for this long-needed
issue.

Hope this helps,

ilan

________________________
Ilan.Samish at weizmann.ac.il
Plant Sciences Department
Weizmann Institute of Science
Tel: 972 8 934 4300
Fax: 972 8 934 4181
Mobile: 972 52 3321150
~~~~~~~~~~~~~~~~~~~
Co-organizer of 3Dsig -
Annual Structural Bioinformatics meeting
http://3Dsig.weizmann.ac.il/
3Dsig at weizmann.ac.il



----- Original Message ----- 
From: "Jeff Cohlberg" <cohlberg at csulb.edu>
To: <molvis-list at bioinformatics.org>
Sent: Tuesday, January 18, 2005 9:53 PM
Subject: [Molvis-list] adding hydrogens to a pdb file


>
> There used to be a WHAT IF web interface in which a user could submit a
> PDB ID number and get back an "hadded.pdb" file with hydrogen atoms
> added.  This site no longer exists, and the WHAT IF software is now only
> available to those who purchase it for 500 Euros (at
> http://swift.cmbi.kun.nl/whatif/).
>
> Is there any other free software or server which can add hydrogens to a
> PDB file?
>
> Jeff Cohlberg
>
> -- 
> Jeffrey A. Cohlberg, Professor
> Department of Chemistry and Biochemistry
> California State University, Long Beach
> 1250 Bellflower Blvd.
> Long Beach, CA 90840
> phone (562) 985-4944   fax (775) 248-1263
>
>
>
>
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