Workflow Entry: mustang provides structural alignment of two proteins

Created at: 20/08/08 @ 14:41:21 Last updated: 25/08/08 @ 15:40:45

Version 3 (latest) (of 3)

Version created on: 20/08/08 @ 14:41:21 by: Steffen Möller | Revision comments Expand

Last edited on: 25/08/08 @ 15:40:46 by: Steffen Möller

Title: mustang provides structural alignment of two proteins

Type: Taverna 1

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Description

This workflow experiments with the partial execution of jobs on a computational grid. The workflow elements "mustang" and "boxshade" are executed on grid nodes. Access to these resources is orchestrated with the plugin available on http://grid.inb.uni-luebeck.de. Please contact the author of this workflow for access permissions.

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Option 1:

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Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

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http://www.myexperiment.org/workflows/377/download?version=3
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Workflow Components

Inputs (2)

Name	Description
1st_protein_id	PDB identifier such as '1rpy'.
2nd_protein_id	PDB identifier such as '1rqq'

Processors (4)

Name	Type	Description
boxshade		Alignment pretty printer
mustang_2		Alignment of two protein structures
2nd_protein_structure	workflow	Retrieves second
1st_protein_structure	workflow	Retrieves first protein structure to investigate

Beanshells (0)

Outputs (5)

Name	Description
alignment_msf	Mustang provides a MSF-formatted sequence alignment that reflects the spatial assignment of residues.
alignment_overlay	A PDB flatfile with the two input structures being spatially aligned.
alignment_pretty	The program boxshade is used to convert the MSF-formatted alignment into a post script file.
1st_protein_structure	The 1st protein structure that was retrieved by its ID (with the nested workflow).
2nd_protein_structure	The 2nd protein structure that was retrieved by its ID (with the nested workflow).

Links (10)

Source	Sink
1st_protein_id	1st_protein_structure:pdbID
2nd_protein_id	2nd_protein_structure:pdbID
1st_protein_structure:pdbFlatFile	mustang_2:pdb_structure_one
2nd_protein_structure:pdbFlatFile	mustang_2:pdb_structure_two
mustang_2:structure_derived_alignment	boxshade:Multiple_Sequence_Alignment_as_MSF
1st_protein_structure:pdbFlatFile	1st_protein_structure
2nd_protein_structure:pdbFlatFile	2nd_protein_structure
boxshade:PostScript_file	alignment_pretty
mustang_2:combined_structures	alignment_overlay
mustang_2:structure_derived_alignment	alignment_msf