Introduction
The decomposition of proteins into structurally distinct units is a common tool for classification and examination of protein structures. TopDomain-Web provides an easy-to-use albeit powerful interface to an suite of techniques for the decomposition of protein structures.
Input
TopDomain-web requires the atomic coordinates of the protein structure to be decomposed. Users can supply coordinates either by uploading files in PDB format or by entering strings that refer to protein structures available from the latest version of PDB, SCOP (release 1.73), CATH (version 3.1.0) or qCOPS (concurrent with latest version of PDB). The syntax of this string allows quick access to major protein structure repositories and is defined as follows:
- <4-letter code>[,chain ID]
- Refers to a protein specified by its 4-letter
code and optional its chain identifier. The tilde symbol (~) is used to
denote chains with a blank chain identifier.
Examples:1dg3
1aqk,L
3fgf,~ - <4-letter code>,<chain ID>,<model number>
- For structures determined by NMR a model number can be specified
in addition. If skipped, TopMatch-web uses the first model found in
the given PDB chain.
Example:1kdx,A,10 - <4-letter code>,<chain fragments>(,<model number>)
- Fragments of a chain can be specified by the PDB residue numbers
of its start and end, separated by a colon (':') and put in
parenthesis. It is valid to specify structures consisting of more than
one fragment in this way. An optional model number may be added for NMR
structures.
Examples:2hhb,A(20:70)
1kdx,A(587:640),10
1bxz,A(1:139)A(314:352)
(the last example corresponds to SCOP domain d1bxza1, see below) - d<4-letter code><chain ID><domain number>
- (=SCOP SID). Refers to a domain of a PDB structure as defined in
the SCOP classification.
Examples:d1sdwa2
d1sdf__ - e<4-letter code><chain ID><2-digit domain number>
- (=CATH Domain ID). Refers to a domain of a PDB structure as defined in
the CATH classification.
Examples:e1sdwA01
e1sdf000 - c<4-letter code><chain ID><domain number>
- (=qCOPS Domain ID). Refers to a domain of a PDB structure as
defined in the qCOPS
classification. Note that qCOPS chain identifiers are case sensitive.
Examples:c3cfdA1
c1qp1C_
