Index of /func/data

      Name                    Last modified       Size  Description


[DIR] Parent Directory        20-Aug-2004 17:59      -  
[TXT] README.txt              30-Mar-2002 02:24     4k  
[TXT] jullookup.txt           17-Feb-2000 15:52    85k  
[TXT] mips_cat_decode.txt     06-Dec-1999 08:50    12k  
[TXT] mips_scop_relate.txt    06-Dec-1999 12:18   632k  
[TXT] pdb100id_to_julpdb.dat  13-Dec-1999 03:05   301k  
[TXT] pdb100id_to_mipspdb.dat 12-Dec-1999 14:42   306k  
[TXT] pdb100id_to_rileypdb..> 12-Dec-1999 14:42   307k  
[TXT] prejullookup.txt        06-Dec-1999 10:06    83k  
[TXT] riley_cat_decode.txt    06-Dec-1999 11:33    13k  
[TXT] riley_scop_relate.txt   06-Dec-1999 11:33    37k  
[TXT] search.txt              30-Mar-2002 01:03    13k  

This directory gives data files carefully cross-referencing three
well-known functional classification systems to structures in scop
(version 1.39).  The functional classification schemes are:

JUL    - Augmented Flybase+ENZYME
RILEY  - GenProtEC functional classification for E coli
MIPS   - MIPS scheme for yeast

(References for all these schemes as well as scop are given in the
PartsList paper, referred to at the bottom.  URLs for current versions
of everything are given on PartsList.org . The files in this 
directory are only a partial view of functional classifications
as they relate to structure. Users should go to home sites
of the functional classifications to get the full classifications.)

#############################
1) Functional Classifications 
#############################

Here are the raw functional classifications in standardized format.
Each file has a slightly different format.

riley_cat_decode.txt
~~~~~~~~~~~~~~~~~~~~
1.5.14  FNT family      1       Cell processes  1.5     Transport/binding protei
1.5.15  FeoB family     1       Cell processes  1.5     Transport/binding protei
1.5.16  GPH family      1       Cell processes  1.5     Transport/binding protei
1.5.17  General PTS family      1       Cell processes  1.5     Transport/bindin
1.5.18  GltS family     1       Cell processes  1.5     Transport/binding protei

111111  222222222222222...
Field 1 is function ID number
Remaining fields give some definition of function

jullookup.txt
~~~~~~~~~~~~~
 D      1.2.9.5.1.1.1   Function Primitive: Metabolism | Process:  Nucleotides a
 D      1.3.1.2  Function Primitive: Metabolism | Process: Protein Metabolism an
 D      1.3.2.4.1.6     Function Primitive: Metabolism | Process: Protein Metabo
 E 4.6.1.10 Class: Lyases | Subclass: Phosphorus-oxygen lyases | Sub-subclass: N
 E 4.6.1.5 Class: Lyases | Subclass: Phosphorus-oxygen lyases | Sub-subclass: No
 E 4.99.1.1 Class: Lyases | Subclass: Other lyases | Sub-subclass: None | Enzyme
 E 5.1.1.1 Class: Isomerases | Subclass: Racemases and epimerases | Sub-subclass
 J      hormone_relaxin Hormone Relaxin
 J      ion_chann_toxin Toxin that blocks ion channels
 J      lipid_transp    Protein that participates in lipid transport
 J      neuro_musc_joint_toxin  Toxin that blocks the excitation of muscles by b

 1 222222222222222222222222222  33333333333333333333333.........
Field 1 is functional classification (D=flybase, E=Enzyme, J=custom)
Field 2 is function ID number
Remaining fields give some definition of function


mips_cat_decode.txt
~~~~~~~~~~~~~~~~~~~
01              METABOLISM
01.01           amino-acid metabolism
01.01.01                amino-acid biosynthesis
01.01.04                regulation of amino-acid metabolism
01.01.07                amino-acid transport
01.01.10                amino-acid degradation

11111111        2222222222222222222222222222222.......
Field 1 is function ID number, either class or subclass
Remaining fields give some definition of function

########################################
(2) Relating Functions to Select PDB IDs
########################################

mips_scop_relate.txt  
riley_scop_relate.txt
prejullookup.txt + jullookup.txt

These three files relate the functional categories in section 1 to
SCOP IDs that have close matches to functionally classified proteins.

#####################################
(3) Relating Functions to All PDB IDs
#####################################

pdb100id_to_julpdb.dat
pdb100id_to_mipspdb.dat
pdb100id_to_rileypdb.dat

These three files relate ALL the known scop IDs (15198) to the scop
IDs that have been classified in section #2.

d1a72_1 d3btoa1 99.6
d1deha1 d1deha1 100
d1dehb1 d1deha1 100
d1htba1 d1deha1 99.6
d1htbb1 d1deha1 99.6
d1hdxa1 d1deha1 100
d1hdxb1 d1deha1 100
d1sra__ d1cpn__ 32.3
d1bmoa1 d1cpn__ 32.3
d1bmob1 d1cpn__ 32.3
d1rro__ d3ctn__ 36.9
1111111 2222222 3333

Field 1 is one of all possible scop IDs.
Field 2 is a scop ID that has been functionally classified.
Field 3 is the precent identity of the match. 

(Note that an identity less than, say, 90% means that one should NOT
use the functional assignment. )

##############
(4) search.cgi 
##############

search.txt
is the actual script that does the lookup for the web form.
It should be renamed search.cgi and given execute permission. 

########
CITATION: J Qian et al. (2001) PartsList. Nuc. Acids Res. 29: 1750-64
########