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| + | ====== CATH List File (CLF) ====== | ||
| + | |||
| + | ===== Format 2.0 ===== | ||
| + | |||
| + | This file format has an entry for each structural entry in CATH. | ||
| + | |||
| + | ^ Column ^ Description ^ | ||
| + | | 1 | CATH domain name (seven characters) | | ||
| + | | 2 | Class number | | ||
| + | | 3 | Architecture number | | ||
| + | | 4 | Topology number | | ||
| + | | 5 | Homologous superfamily number | | ||
| + | | 6 | S35 sequence cluster number | | ||
| + | | 7 | S60 sequence cluster number | | ||
| + | | 8 | S95 sequence cluster number | | ||
| + | | 9 | S100 sequence cluster number | | ||
| + | | 10 | S100 sequence count number | | ||
| + | | 11 | Domain length | | ||
| + | | 12 | Structure resolution (Angstroms) \\ (999.000 for NMR structures and 1000.000 for obsolete PDB entries) | | ||
| + | |||
| + | Comment lines start with a '#' character. | ||
| + | |||
| + | |||
| + | ==== Example ==== | ||
| + | |||
| + | <code> | ||
| + | 1oaiA00 1 10 8 10 1 1 1 1 1 59 1.000 | ||
| + | 1go5A00 1 10 8 10 1 1 1 1 2 69 999.000 | ||
| + | 1oksA00 1 10 8 10 2 1 1 1 1 51 1.800 | ||
| + | 1t6oA00 1 10 8 10 2 1 2 1 1 49 2.000 | ||
| + | 1cuk003 1 10 8 10 3 1 1 1 1 48 1.900 | ||
| + | 1hjp003 1 10 8 10 3 1 1 2 1 44 2.500 | ||
| + | 1c7yA03 1 10 8 10 3 1 1 2 2 48 3.100 | ||
| + | 1p3qQ00 1 10 8 10 4 1 1 1 1 43 1.700 | ||
| + | 1mn3A00 1 10 8 10 4 1 2 1 1 52 2.300 | ||
| + | 1nv8B01 1 10 8 10 5 1 1 1 1 71 2.200 | ||
| + | </code> | ||
| + | |||
| + | ==== CATH Domain Names ==== | ||
| + | |||
| + | The domain names have seven characters (e.g. 1oaiA00). | ||
| + | |||
| + | ^ Characters ^ Description ^ | ||
| + | | 1-4 | PDB Code \\ The first 4 characters determine the PDB code e.g. 1oai | | ||
| + | | 5 | Chain Character \\ This determines which PDB chain is represented. | | ||
| + | | 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. | | ||
| + | |||
| + | |||
| + | ==== Hierachy Node Representatives ==== | ||
| + | |||
| + | Representative structural domains are selected from the CathDomainList based on | ||
| + | the numbering scheme. For example the S35 sequence family representatives | ||
| + | for superfamily 1.10.8.10 in the above example are 1oaiA00, 1oksA00, 1cuk003, | ||
| + | 1p3qQ00 and 1nv8B01 as these are the first instances in the file with the same | ||
| + | superfamily number i.e. 1.10.8.10 but all have different S35 numbers (1 to 5). | ||
| + | |||
