Create custom-made GPCR alignments

Created: 2010-08-24 13:58:32 Last updated: 2010-08-24 13:58:35

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This workflow allows you to create your own GPCR alignments. The alignments are built from the residues that are annotated with the general residue numbers. Alignments are therefore not built using standard alignment algorithms but are created by selecting residues that are likely to share the same position in the three-dimensional structure. Users can select the proteins and residue positions that should be aligned, allowing for the creation of e.g. an alignment of all binding pocket residues of all human adrenoceptors.

Input is a list of proteins and a list of residue numbers in the GPCRDB residue numbering scheme. If you are using Ballesteros-Weinstein numbers you can convert these to GPCRDB number by using our conversion service.

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Inputs (2)

Name	Description
proteinIds
residueNumbers

Processors (3)

Name	Type	Description
createAlignment	wsdl	Wsdl http://www.gpcr.org/7tm/webservice/?wsdl Wsdl Operation createAlignment
inputParameters	xmlsplitter
output	xmlsplitter

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Outputs (1)

Name	Description
alignmentFasta

Datalinks (5)

Source	Sink
inputParameters:output	createAlignment:parameters
proteinIds	inputParameters:proteinIds
residueNumbers	inputParameters:residueNumbers
createAlignment:parameters	output:input
output:return	alignmentFasta

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Taverna 2

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Bas Vroling

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Bas Vroling

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1625 viewings

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Create custom-made GPCR alignments

Created by Bas Vroling on Tuesday 24 August 2010 13:58:32 (UTC)

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Other workflows that use similar services (2)

Taverna 2

Uploader

Bas Vroling

Retrieve a protein from the GPCRDB (1)

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This small workflow illustrates how to use the web service access provided by the GPCRDB in Taverna. The proteinId input field is case sensitive and by default the identifiers in the GPCRDB are lowercase. You can try this mini-workflow with e.a. 'adrb2_human'.