[Molvis-list] adding hydrogens to a pdb file

[Ilan Samish]

Hi Jeff,

This is just another example of the unbridgable clash between artificial and
human intelligence. In REDUCE there is a possibility to place hydrogens on
all possible places and then the user can decide whether the local pH
requires the hydrogens and if so, what tautomer to use.

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
~~~~~~~~~~~~~~~~~~~
----- Original Message ----- 
From: "Jeff Cohlberg" <cohlberg at csulb.edu>
To: "Molecular Visualization, especially in education with freeware"
<molvis-list at bioinformatics.org>
Sent: Wednesday, January 19, 2005 8:37 PM
Subject: Re: [Molvis-list] adding hydrogens to a pdb file


> Another difference:  When I use the file 1AB9 (chymotrypsin with bound
> pentapeptide) and look at the charge relay system (asp102, his57,
> ser195), WHAT IF puts both the histidine and the serine in the
> protonated form, and REDUCE puts both in the unprotonated form.  Of
> course the protonation state depends on what stage of the catalytic
> cycle you're in, but at no stage are both the histidine and serine
> protonated.  Anyway, I find this difference curious -- apparently the
> different programs use different criteria for deciding which residues to
> protonate.
>
> Jeff
>
>
>
> Ilan Samish wrote:
>
> >As much as I admire Deep View, for hydrogens it does not do an extensive
> >search to locate the best position. This is unlike YASARA (that we never
> >checked) and REDUCE.
> >Notably, such searches often result in a decision that the side chain
should
> >be flipped (more than 20% of Asn/Gln in high-resolution structures
undergo
> >such flips). This may also lead to a totally different H-bond pattern for
> >polar/negative residues.
> >ilan
> >
> >----- Original Message ----- 
> >From: "Annemarie Honegger" <honegger at bioc.unizh.ch>
> >To: <cohlberg at csulb.edu>; "Molecular Visualization, especially in
education
> >with freeware" <molvis-list at bioinformatics.org>
> >Sent: Wednesday, January 19, 2005 12:02 PM
> >Subject: Re: [Molvis-list] adding hydrogens to a pdb file
> >
> >
> >
> >
> >>For example Deep View (Swiss PDB Viewer) http://www.expasy.org/spdbv/
> >>
> >>
> >>Annemarie Honegger
> >>
> >>
> >>
> >
> >
> >
> >----- Original Message ----- 
> >From: "Ilan Samish" <ilan.samish at weizmann.ac.il>
> >To: <cohlberg at csulb.edu>; "Molecular Visualization, especially in
education
> >with freeware" <molvis-list at bioinformatics.org>
> >Sent: Wednesday, January 19, 2005 11:37 AM
> >Subject: Re: [Molvis-list] adding hydrogens to a pdb file
> >
> >
> >
> >
> >>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
> >>>
> >>>
> >>>
> >>>
> >>>_______________________________________________
> >>>Molvis-list mailing list
> >>>Molvis-list at bioinformatics.org
> >>>https://bioinformatics.org/mailman/listinfo/molvis-list
> >>>
> >>>
> >>>
> >>_______________________________________________
> >>Molvis-list mailing list
> >>Molvis-list at bioinformatics.org
> >>https://bioinformatics.org/mailman/listinfo/molvis-list
> >>
> >>
> >>
> >
> >_______________________________________________
> >Molvis-list mailing list
> >Molvis-list at bioinformatics.org
> >https://bioinformatics.org/mailman/listinfo/molvis-list
> >
> >
> >
>
> -- 
> 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
>
>
>
> _______________________________________________
> Molvis-list mailing list
> Molvis-list at bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/molvis-list
>