SecStrAnnotator:OneToOne

SecStrAnnotator finds annotation for a query protein Q, based on the template protein T. Thus, the input consists of the structure of T, structure of Q, and annotation of T.

The annotation algorithm consists of three major steps. The first step is structural alignment and superimposition of the query protein with the template protein, so the corresponding parts of the two proteins are located close to each other. In the second step, secondary structure assignment (SSA) is performed – SSEs are detected in the query protein Q. The third step is called matching – the algorithm will match the template SSEs to the query SSEs and for each annotated SSE in T it will select the corresponding SSE in Q.

Execution

SecStrAnnotator is executed from command line and can run on both Windows and Unix. However, on Unix system it must be run using Mono.

Windows:

SecStrAnnotator.exe [OPTIONS] DIRECTORY TEMPLATE QUERY

Unix:

mono SecStrAnnotator.exe [OPTIONS] DIRECTORY TEMPLATE QUERY

Arguments

• DIRECTORY is the directory containing all the input files. The output files will also be saved to this directory.
• TEMPLATE describes the template protein domain in one of the following formats: PDB or PDB,CHAIN or PDB,CHAIN,RANGES. The whole argument must be written without spaces. Examples:
  • 1og2 (structure 1og2, chain A by default)
  • 1og2,B (chain B)
  • 1og2,B,100:400 (residues 100–400 of the chain B)
  • 1og2,B,:400 (residues up to 400 of the chain B)
  • 1h9r,A,123:183,252:261 (residues 123–183 and 252–261 of the chain A)
• QUERY describes the query protein domain and uses the same format as TEMPLATE.

Options

There is a range of options which can be used to modify the behaviour of SecStrAnnotator. The most important option is:

• --help Prints the help message, which includes the description of all other options.