[Molvis-list] adding hydrogens to a pdb file

[Jeff Cohlberg]

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
>>>
>>>
>>>
>>>
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>>>
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>
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>  
>

-- 
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