Uniprot Protein Visualization

Created: 2010-05-01 20:29:37 Last updated: 2010-05-01 20:40:10

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Jmol 3D visualization of a protein structure.

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Workflow Components

Authors (1)

Titles (2)

Descriptions (1)

Dependencies (0)

Inputs (0)

Processors (6)

Name	Type	Description
UniProt_Record_value	stringconstant	Value P68871
fetch_jmol_file	workflow
limit	beanshell	Script output = new ArrayList();int limitInt = Integer.parseInt(limit);for (int i = 0; i < input.size() && limitInt > 0; i++) { List list = (List) input.get(i); for (int j = 0; j < list.size() && limitInt > 0; j++) { output.add(list.get(j)); limitInt--; }}
limit_value	stringconstant	Value 5
UniProt-to-PDB	sadi	Endpoint http://biordf.net/sparql
renderProteinStructure	sadi	Endpoint http://biordf.net/sparql

Beanshells (2)

Name	Description	Inputs	Outputs
limit		limit input	output
selectLastUrl		in	out

Outputs (1)

Name	Description
hasJmol3DStructureVisualization

Datalinks (6)

Source	Sink
limit:output	fetch_jmol_file:jmol_file_location
limit_value:value	limit:limit
renderProteinStructure:hasJmol3DStructureVisualization (Thing)	limit:input
UniProt_Record_value:value	UniProt-to-PDB:UniProt_Record
UniProt-to-PDB:has3DStructure (PDB_Record)	renderProteinStructure:PDB_Record
fetch_jmol_file:jmol_file	hasJmol3DStructureVisualization

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

David Withers

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

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Information Tags (3)

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pdb
|
sadi
|
uniprot

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Information Shared with Groups (1)

SADI

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Information Favourited By (1)

Mark Wilkinson

Information Statistics

2377 viewings

1609 downloads

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Citations (0)

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Version History

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Uniprot Protein Visualization

Created by David Withers on Saturday 01 May 2010 20:29:37 (UTC)

Last edited by David Withers on Saturday 01 May 2010 20:40:11 (UTC)

Reviews (2)

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Kasikrit Damkliang

Title: Service unavailable

Rating: not yet rated

Created: 2015-07-29 09:36:53 | Updated: 2015-07-29 09:36:53

I just found that UniProt-to-PDB and renderProteinStructure is not working.How can I fix it or use other services instead?Best Regards,Kasikrit

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Mark Wilkinson

Title: Ideas for extension of the workflow

Rating: 5 out of 5

Created: 2011-02-17 19:49:14 | Updated: 2011-02-17 19:50:28

works exactly as indicated. Input is the UniProt ID of any protein of interest. To extend this workflow futher, you can add the SADI KEGG Pathway -> KEGG Genes service, then KEGG Genes -> UniProt IDs service. This will then give you the jMol visualization of all of the proteins in a given pathway. Very very cool :-)

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