Structural alignment of arbitrary number of protein structures.

Created: 2008-09-02 14:59:23

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This grid-executed Mustang application performs a structural alignment of protein sequences. The number of arguments is variable, in principle, but is shown here for three. The application is executed via the Taverna-ARC plugin on a machine of the NorduGrid. Although your machine can be a part of it, you may prefer to wait for a later version of that interface that does not require grid certificates.

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Workflow Components

Inputs (3)

Name	Description
1st structure PDB ID	A PDB ID like '1va1'. The corresponding PDB entry is fetched from the database.
2nd structure PDB ID	A PDB ID like '1va2. The corresponding PDB entry is fetched from the database.
3rd structure PDB ID	A PDB ID like '1va3'. The corresponding PDB entry is fetched from the database.

Processors (4)

Name	Type	Description
Mustang_Structure_Alignment		structural alignment of arbitrary number of protein structures
2nd	workflow
3rd	workflow
1st	workflow

Beanshells (0)

Outputs (7)

Name	Description
stdout	Standard output of mustang.
stderr	Error messages are presented here. If there are any, then these should be forwarded to the author of this workflow.
combined structures	Overlay of all structurally aligned structures.
structure_derived_sequence_alignment	A protein sequence alignment that has its assignment primarily in the spacial vicinity of the corresponding amino acids in the protein structure alignment.
1st_structure	The first structure that was retrieved from PDB.
2nd_structure	The second structure that was retrieved from PDB.
3rd_structure	The third structure that was retrieved from PDB.

Links (13)

Source	Sink
1st structure PDB ID	1st:pdbID
2nd structure PDB ID	2nd:pdbID
3rd structure PDB ID	3rd:pdbID
1st:pdbFlatFile	Mustang_Structure_Alignment:pdb_structures
2nd:pdbFlatFile	Mustang_Structure_Alignment:pdb_structures
3rd:pdbFlatFile	Mustang_Structure_Alignment:pdb_structures
1st:pdbFlatFile	1st_structure
2nd:pdbFlatFile	2nd_structure
3rd:pdbFlatFile	3rd_structure
Mustang_Structure_Alignment:STDERR	stderr
Mustang_Structure_Alignment:STDOUT	stdout
Mustang_Structure_Alignment:combined_structures	combined structures
Mustang_Structure_Alignment:structure_derived_alignment	structure_derived_sequence_alignment