Where to find PDB-like datafiles for misfolded structures?
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.
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
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
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
Hope you find this useful.
_/ C.S.RAMAN _/
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