From raman "-at-" bioc01.uthscsa.edu Fri Nov 12 00:25:56 1993 Received: from thorin.uthscsa.edu for raman -A_T- bioc01.uthscsa.edu by www.ccl.net (8.6.1/930601.1506) id AAA10401; Fri, 12 Nov 1993 00:16:09 -0500 Received: from bioc01.uthscsa.edu by thorin.uthscsa.edu with SMTP; Thu, 11 Nov 1993 23:16:55 -0600 (CST) Received: by bioc01.uthscsa.edu (4.1/SMI-4.1) id AA27645; Thu, 11 Nov 93 23:16:37 CST From: raman /at\bioc01.uthscsa.edu (C.S.RAMAN) Message-Id: <9311120516.AA27645 |-at-| bioc01.uthscsa.edu> Subject: Re:Misfolded Protein Structures.... To: PATTABIR&$at$&FCRFV1.NCIFCRF.GOV (N. Pattabiraman) Date: Thu, 11 Nov 1993 23:16:37 -0600 (CST) Cc: chemistry ^%at%^ ccl.net X-Mailer: ELM [version 2.4 PL3] Content-Type: text Content-Length: 2839 Dear Pattabi: Although I don't have any misfolded structures to provide you at the moment, the following might be the next best thing I would suggest. It should get you started. 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 ............................................................................. The best way to get these structures is via gopher. Follow the procedure given below to accomplish the same: 1. gopher ftp.embl-heidelberg.de 2. choose #3 on the menu 3. #2 databases 4. #24 protein-extras 5. #4 misfolded 6. This directory has a README file (excerpted above) as its last entry and the others are the misfolded structures in the pdb format. If you have trouble downloading via gopher, then, ftp to the same site to get the files you want. Good luck and let me know if you have difficulty in downloading the files. Regards -raman -- C.S.Raman raman $#at#$ bioc01.uthscsa.edu - Internet UNIX Programming & Administration 70412.2354:~at~:compuserve.com - CIS SPARC & SGI Systems raman -x- at -x- hermes.chpc.utexas.edu - CHPC Department of Biochemistry c.raman ":at:" launchpad.unc.edu UTHSCSA 7703 Floyd Curl Dr. (210) 567-6623 [Tel] San Antonio, TX 78284-7760 (210) 567-6595 [Fax] ****************************************************************************** If a man's wit be wandering, let him study the Mathematics -Francis Bacon ******************************************************************************