Where to find PDB-like datafiles for misfolded structures?

C.S.RAMAN raman at BIOC01.UTHSCSA.EDU
Tue Mar 28 11:49:36 EST 1995


> Info about misfolded proteins from Sander (J.Mol.Biol.) was
> presented in a very accurate (due to implemented pair comparison
> approach) manner: pairs of potentially misfolded entries without 
> exact reference which one of them is wrong (in addition, some 
> of listed entries are absent in current PDB).
> 
> So, how to find PDB (or similar) datafiles for knowlingly
> misfolded structures (or partially misfolded, with some
> wrong chain placement or domain structure)?

The deliberately misfolded structures from Chris Sander's group ARE
following URL.  These files can also be retrieved via FTP and through
the WEB server at EMBL.


#
Type=0+
Name=README
Path=0/pub/databases/protein_extras/misfolded/README
Host=gopher.EMBL-Heidelberg.DE
Admin=EMBL Computer Group <unixadmin at embl-heidelberg.de>
ModDate=Thu Nov 26 01:00:00 1992 <19921126010000>

I am including the README file here for your infomation.

Database of deliberately misfolded protein models
-------------------------------------------------

reference: 
Holm, L., Sander, C. (1992) Evaluation of protein models by atomic solvation 
preference.  J. Mol. Biol. 225, 93-105.

The models were generated by selecting pairs of known structures which
have an equal number of residues.  The backbone conformation of the crystallo-
graphic structure was kept, but the sequences were swapped and side chains
optimized using a fast Monte Carlo algorithm with a simple energy function.
The misfolded models were then subjected to 500 steps of steepest descents 
energy minimization using the GROMOS program.

The models are named AAAAonBBBB, where AAAA is the Protein Data Bank (PDB)
identifier for the sequence and BBBB is the PDB identifier of the backbone 
coordinates.

1bp2on2paz.brk   1cbhon1ppt.brk   1fdxon5rxn.brk   1hipon2b5c.brk   
1lh1on2i1b.brk   1p2pon1rn3.brk   1ppton1cbh.brk   1reion5pad.brk   
1rhdon2cyp.brk   1rn3on1p2p.brk   1sn3on2ci2.brk   1sn3on2cro.brk   
2b5con1hip.brk   2cdvon2ssi.brk   2ci2on1sn3.brk   2ci2on2cro.brk   
2croon1sn3.brk   2croon2ci2.brk   2cypon1rhd.brk   2i1bon1lh1.brk   
2pazon1bp2.brk   2ssion2cdv.brk   2tmnon2ts1.brk   2ts1on2tmn.brk
5padon1rei.brk   5rxnon1fdx.brk   


Hope you find this useful.
Cheers
-raman
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   _/                           C.S.RAMAN                                  _/
   _/                   Department of Biochemistry                         _/
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