Re: [Psisoft-devl] high contact

[Wan K. K. <kim...@bi...>]

Hi,

I would like to add a few PDBugs.

# next if ($mpdb =~ /^(1cwq|1e0p|1gtw|1cm4)$/) ; ### same model with 
different chain identifier

I am using PQS coordinates for X-ray crystallography structures,
which solves many such problems (i.e. 1g7y is splitted into 3 files 
without overlap.)

cheers

wan

>The solution (in my experience) is to just apply manual filtering of such
>structures after applying statistics. When I find these things I delete
>them from my psimap database.
>
>These things are so abhorrent they generally skew any analysis by miles,
>allowing us to recognize the problem immediatly.
>
>This mailing list is the perfect place to keep up to date on 'problem
>structures', as subtle different analysis can show up different problems.
>
>
>For example I have the following code in my psimaper...
>
>my $st  = "
>  SELECT a.PDB, a.SUNID, a.DOMAIN, a.NEAT_SCCS
>  FROM $scopDb.domain a                 # Domain table
>  INNER JOIN $pdbDb.pdb b               # PDB table
>  ON a.PDB = b.PDB
>  WHERE (
>    b.TYPE = 'X-RAY DIFFRACTION'                # PDB criteria
>#    OR b.TYPE = 'SYNCHROTON DIFFRACTION'       #
>#    OR b.TYPE = 'NMR'                          #
>#    OR b.TYPE = 'ELECTRON MICROSCOPY'          #
>#    OR b.TYPE = 'NEUTRON DIFFRACTION'          #
>#    OR b.TYPE = 'FIBER DIFFRACTION'            #
>#    OR b.TYPE = 'THEORETICAL MODEL'            #
>#    OR b.TYPE = 'FLUORESCENCE'                 #
>  )                                             #
>#   AND  b.RESOLUTION < 2                       #
>  ";
>
>The above helps a lot with subsequent domain assignment.
>
>And...
>
>  next if $pdb eq '1gtv';   # Multi-Model PDB entries
>  next if $pdb eq '1cm4';   #
>  next if $pdb eq '1cwq';   #
>  next if $pdb eq '1e0p';   #
>  next if $pdb eq '1gu8';   #
>
>  next if $pdb eq '4cpa';   # Contains null chain AND 
>                            # named chain!
>                            # PDB stubournly refuse to fix,
>                            # so you should complain!
>
>
>  next if $pdb eq '1g7y';   # Contain 'significant' 
>  next if $pdb eq '1ygp';   # crystal overlap between
>  next if $pdb eq '1hb9';   # subunits - PDB will fix.
>  next if $pdb eq '1hb5';   # 
>
>
>I see that they don't fully overlap with yours which is interesting. We
>should make a community webpage to name and same these pdb structures.
>
>I call it PDBug, lets set up a Bugzilla! 
>
>
>
>I am doing a simple analysis of interface density, where I compare the
>number of residues on each side of a domain-domain interface (a simple
>plot shows an interesting trend). This analysis showed up this problem
>structure...
>
>1ona
>
>Which is a problem both in the PDB and with my domain parser... Anyway it
>has an unnatural 'domain interface' mediated by a mis-labeled ligand.
>
>
>Is Wan a psimapper? I bet he knows of some PDB problems.
>
>
>All the above problems should be fixed by using MSD. I am planning to
>write an O-rily book (mini) called 'MSD', basically because I like the
>idea of adding a virus into the O-rily taxonomy (using a picture of a
>virus from the 3D structure in MSD).
>
>We should start using MSD with PSIMAP ASAP. We can write the book after
>that. MSD will ...
>
> Fix multimodel PDB / NMR structures.
> Fix problems mapping PDB to SwissProt.
> Automatically provide sequence / sturcture alignments.
> Provide clean ;) SCOP/CATH/PFAM/DALI (e-family) assignments to structues.
> Provide clean ligand assignments to stuctures.
> Give us 'biomolecule' data
> Filter crystal contacts
> Do away with the need for parsers in PSIMAP.
> Allow easy integration of domain-domain, domain-ligand and ligand-ligand
>information
>
> etc., etc.
>
>
>
>P.S. I did an analysis of residue connectivity statistics for a second
>year report. 
>
>
>You can find this at...
>
>http://interaction.mrc-dunn.cam.ac.uk/Scientists/Dan_Bolser/MyDoc/New%20Folder/
>
>(I may change the folder name without warning.)
>
>
>Just let me know if you want to turn this into a paper with some extra
>work (actually it looks quite comprehensive). I can work closly with
>anyone on this topic, as I still remeber the literature and the problems
>in detail.
>
>I am half planning to revive this report into a thesis chapter anyway, so
>any help I can get would be great ;)
>
>
>All the best,
>Dan.
>
>
>
>On Wed, 11 Aug 2004, Andreas Henschel wrote:
>
>  
>
>>Hi psimap folks,
>>
>>I found some pdb entries that look like superimposed structures, a 
>>structural alignment of very similar  (they are not NMR!)
>>that cause trouble to psimap. One of them is 1cm4.  I found out about 
>>them when I counted contacts per residue and some where as high as 50, 
>>thus falsifying my hotspot statistics.
>>
>>Also, these guys have suspiciuosly high contact residues:
>>| 1ae6   |
>>| 1bwm   |
>>| 1cm4   |
>>| 1cr9   |
>>| 1cu4   |
>>| 1eo8   |
>>| 1ob1   |
>>| 1qfu   |
>>For the moment, I will ignore them.
>>Any idea?
>>Cheers,
>>Andreas
>>
>>
>>
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>>
>>    
>>
>
>  
>


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* Wan Kyu Kim                                *
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