[Molvis-list] adding hydrogens to a pdb file

[Tamas E. Gunda]

You may want to try Mol2Mol (http://web.interware.hu/frenzy/mol2mol), although it is
shareware, not freeware. It adds hydrogens in "half-artificial" pH dependent mode, i.e.
you have to decide in advance to protonate or not  -NH2, -SH, -COOH etc. groups.

By the way, the problem with protonation of PDB files is that geometric data are often not
precise enough, there are often bigger faults too. If the program would depend mainly or
solely on the residue info, some obvious flaws could be eliminated, however, this is an
impracticable way as residue info often misses. Therefore not only bond length and angle
info have to be considered but pyramidality, dihedral etc values as well.

Prof. Tamas E. Gunda
University of Debrecen
Medical and Health Science Center
Dept. of Pharmaceutical Chemistry
POBox 36
H-4010 Debrecen
Hungary
e-mail: tgunda {A.T} puma.unideb.hu



----- 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: Thursday, January 20, 2005 11:22 AM
Subject: Re: [Molvis-list] adding hydrogens to a pdb file


> 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
> >
> >
> >
> > _______________________________________________
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> > Molvis-list at bioinformatics.org
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> >
>
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