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--- data:cathdomaindescriptionfile [2008/09/16 07:24] – garner
+++ data:cathdomaindescriptionfile [2014/11/07 14:56] (current) – sillitoe
@@ Line 1: / Line 1: @@
+====== Cath Domain Description File (CDDF) ======
+===== Format 1.0 =====
+Each entry corresponds to a CATH domain for a given release of the CATH database.
+Note: Different releases of CATH may have different domain definitions.
+See below for CATH domain and segment naming conventions.
+Information is compiled from the following files:
+  * [[CathDomainList]]
+  * [[CathDomall]]
+  * CathDomain Fasta Sequences
+  * CathSegment Fasta Sequences
+  * PdbSum file (in CDDF format)
+  * ChainLimits file (in CDDF format)
+Comment lines start with a '#' character.
+MAXIMUM of 80 characters per line (composed of a tag that is always a maximum of
+characters; the rest of the line should be no longer than 70 characters).
+^ Tags  ^ Description  ^
+| FORMAT   | Format definition (CDDF1.0) and first line of each entry   |
+| DOMAIN   | CATH domain identifier - six character code (e.g. 1abc01)  |
+| PDBID	   | PDB identifier - four character code  \\ (currently only used in PdbSumData files)   |
+| VERSION  | CATH version number          |
+| VERDATE  | CATH version release date    |
+| NAME	   | PDB entry description         |
+| SOURCE   | PDB entry organism/source    |
+| CATHCODE | CATH superfamily code C.A.T.H e.g. 1.10.10.10   |
+| CLASS	   | Text description of class level (default: 'void')   |
+| ARCH	   | Text description of architecture level (default: 'void')   |
+| TOPOL	   | Text description of topology level (default: 'void')   |
+| HOMOL	   | Text description of homologous superfamily level (default: 'void')  |
+| DLENGTH  | Length of the domain sequence    |
+| DSEQH	   | Domain sequence header in FASTA format (e.g. '>pdb%%|%%1abc01')   |
+| DSEQS	   | Domain sequence string in FASTA format    |
+| NSEGMENTS | Number of segments that comprise the domain (integer)   |
+| SEGMENT   | Segment identifier (e.g. 1abc01:1:2)    |
+| SRANGE    | Start and stop PDB residue identifiers that define the range of segment \\ (e.g. START=159  STOP=202)    |
+| SLENGTH   | Length of the segment sequence     |
+| SSEQH	    | Segment sequence header in FASTA format (e.g. '>pdb%%|%%1abc01:1:2')    |
+| SSEQS	    | Segment sequence string in FASTA format    |
+| ENDSEG    | Signifies end of segment entry    |
+| COMMENTS  | Text    |
+| %%//%%    | Signifies end of entry    |
+==== Example ====
+<code>
+FORMAT    CDDF1.0
+DOMAIN    9lprA1
+VERSION   2.4
+VERDATE   14-Jan-2002
+NAME      Alpha-lytic protease complex with methoxysuccinyl- Ala- Ala- Pro- Leuc
+NAME      ine boronic acid
+SOURCE    (Lysobacter enzymogenes 495) cloned and expressed in (escherichia coli
+SOURCE    )
+CATHCODE  2.40.10.10
+CLASS     Mainly Beta
+ARCH      Barrel
+TOPOL     Thrombin, subunit H
+HOMOL     Trypsin-like serine proteases
+DLENGTH   87
+DSEQH     >pdb|9lprA1
+DSEQS     IVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSA
+DSEQS     QTLLLQPILSQYGLSLV
+NSEGMENTS 2
+SEGMENT   9lprA1:1:2
+SRANGE    START=16   STOP=115
+SLENGTH   74
+SSEQH     >pdb|9lprA1:1:2
+SSEQS     IVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSA
+SSEQS     QTLL
+ENDSEG
+SEGMENT   9lprA1:2:2
+SRANGE    START=231  STOP=242
+SLENGTH   13
+SSEQH     >pdb|9lprA1:2:2
+SSEQS     LQPILSQYGLSLV
+ENDSEG
+COMMENTS  Blah Blah
+//
+</code>
+NOTE:
+The following CATH hierarchy description lines are typically found together
+(derived from CathList and CathNames files)
+<code>
+CATHCODE  2.40.10.10
+CLASS     Mainly Beta
+ARCH      Barrel
+TOPOL     Thrombin, subunit H
+HOMOL     Trypsin-like serine proteases
+</code>
+The following domain sequence lines are typically found together
+(derived from CathDomain Fasta Sequence File)
+<code>
+DLENGTH   87
+DSEQH     >pdb|9lprA1
+DSEQS     IVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSA
+DSEQS     QTLLLQPILSQYGLSLV
+</code>
+Segment sequence lines are always initiated with a 'SEGMENT' tag
+and terminated with an 'ENDSEG' tag. The number of segments in the domain
+always precedes the first segment using the 'NSEGMENTS' tag.
+The following segment sequence lines are typically found together
+(derived from CathSegments Fasta Sequence File)
+<code>
+SEGMENT   9lprA1:1:2
+SRANGE    START=16   STOP=115
+SLENGTH   74
+SSEQH     >pdb|9lprA1:1:2
+SSEQS     IVGGIEYSINNASLCSVGFSVTRGATKGFVTAGHCGTVNATARIGGAVVGTFAARVFPGNDRAWVSLTSA
+SSEQS     QTLL
+ENDSEG
+</code>
+===== Cath Domain and Segment Naming Conventions =====
+==== CATH Domain Names ====
+The domain names have seven characters (e.g. 1oaiA00).
+<code>
+CHARACTERS 1-4: PDB Code
+The first 4 characters determine the PDB code e.g. 1oai
+CHARACTER 5: Chain Character
+This determines which PDB chain is represented.
+Chain characters of zero ('0') indicate that the PDB file has no chain field.
+CHARACTER 6-7: Domain Number
+The domain number is a 2-figure, zero-padded number (e.g. '01', '02' ... '10', '11', '12'). Where the domain number is a double ZERO ('00') this indicates that the domain is a whole PDB chain with no domain chopping.
+</code>
+==== CATH Segment Names ====
+CATH segments (continuous regions of sequence within a domain) are described
+adding colon separated numbers to the end of the domain name.
+The first number is the sequential number of the segment.
+The second number is the total number of segments in this domain.
+<code>
+abcA01:1:2
+xxxxxxxooooo
+x = standard CATH six character domain name
+o = segment information :ThisSegment:TotalSegments
+</code>

CATH

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