This file describes a comparison of the fold assignments by various
groups. It is associated with the following paper:

SA Teichmann, C Chothia & M Gerstein (1999).  "Advances in Structural
Genomics," Curr. Opin. Struc. Biol.  9: 390-399.

------------------
Some general notes
------------------

* Many of these assignments were taken from web pages and consequently
may reflected substantially different results from those in the
referred to papers.

* Except for the "Sarah" assignments, all the work refers to the
original 468 ORF file created by TIGR and scop 1.35 or earlier.

* We are happy to update this file. Please contact
sat@mrc-lmb.cam.ac.uk, chc1@mrc-lmb.cam.ac.uk, or
Mark.Gerstein@yale.edu.

* The format looks like this:

who     gid_    orfstrt_        orfstop pdb     pdbstrt pdbstop score   remark  remark2 yu_rem

MG001   364
>C
6-104s
113-241s
242-364s
sarah   MG001   6       104     d2pola1 21      119     4.81.1.1.1
bork    MG001   6       267     2POL-A  110     365     4.81.1.1.1
sarah   MG001   113     241     d2pola2 1       122     4.81.1.1.1
sarah   MG001   242     364     d2pola3 1       121     4.81.1.1.1
kptp    MG001   98      364     1wai    113     365     theoretical model
fisch   MG001   -       -       2pola   -       -       4.81.1.1.1
koonin  MG001   148     258     d2polb3 -       -       4.81.1.1.1

where:

>P=partial match
>C=complete match
s=supported
u=unsupported
*different assignments*

---------------------------
The sets of assignments are
---------------------------

sarah = 
The "sarah" set is used as a reference in the Current Opinion
paper. This is the set of very recently (early 1999) determined
assignments based on PSI blast and scop 1.38. It is described in
detail on the following websites:
http://www.mrc-lmb.cam.ac.uk/genomes/MG
http://bioinfo.mbb.yale.edu/genome/MG

bork = 
Huynen, M, Doerks, T, Eisenhaber, F, Orengo, C, Sunyaev, S, Yuan, Y,
Bork, P. (1998) J. Mol. Biol., 280, 323-326.
http://dove.embl-heidelberg.de/3D

koonin = 
Wolf, YI, Brenner, SE, Bash, PA, Koonin, EV. (1999) Genome Res, 9, 17-26.
ftp://ftp.ncbi.nlm.nih.gov/pub/koonin/FOLDS/index.html
(Based on scop 1.35.)

kptp = 
Rychlewski, L, Zhang, BH, Godzik, A (1998) Fold & Des, 3, 229-238.
http://cape6.scrips.edu/lezek/genome/cgi-bin/genome.pl?mp

fisch = 
Fischer D and Eisenberg, D. (1997) Proc. Natl. Acad. Sci. USA , 94, 11929-11934.
http://www.doe-mbi.ucla.edu/people/frsvr/preds/MG/MG.html
  
jones= 
Jones, DT (1999) J. Mol. Biol., 287, 797-815. ONLY unsupported matches

fasta =
a representative of early FASTA matches using scop 1.32. 
Gerstein, M. (1997) J. Mol. Biol., 274, 562-576.
http://http://bioinfo.mbb.yale.edu/genome/new/db/MG

pdbisl = 
only unsupported matches found by a PSI-BLAST library search with MG
sequences as queries.
http://cyrah.med.harvard.edu/Serv/Servers/ISS/ISS_server.html

pdbT98 = 
SAM-T98 iterative Hidden Markov Model search procedure with pdb domain
as query.  Karplus, K, Barrett, C, Hughey, R. (1998) Bioinformatics
14, 846-856.
http://www.cse.ucsc.edu/research/compbio/HMM-apps/T98-query.html

MGT98 = 
SAM-T98 iterative Hidden Markov Model search procedure with MG sequence as query.
http://www.cse.ucsc.edu/research/compbio/HMM-apps/T98-query.html