The ELM Resource Structure Filter

This web service is useful for evaluating the location of candidate short regulatory sequences in proteins (linear motifs) which need to be accessible to interact with their ligand domains. The StructureFilter web-service calculates an accessibility score, secondary structure score and total score (as well as various other features) for each match of a regular expression or ELM in the query sequence for which structural information is available. (If a regular expression match is determined as having no associated structural information available, no reference is made to this match in the result set.)
the web service consists of three methods:
- RunJob
- GetStatus
- GetResult
Reference:
A structure filter for the Eukaryotic Linear Motif Resource
Allegra Via, Cathryn M Gould, Christine Gemuend, Toby J Gibson and Manuela Helmer-Citterich
BMC Bioinformatics, 2009 (in review)
StructureFilter
Namespace: http://structureFilter.embl.de/StructureFilter
This WSDL file describe the Structure Filter Web Service. It calculates an accessibility score, secondary structure score and total score(as well as various other features) for each match of a regular expression or ELM in the query sequence for which structural information is available. If a regular expression match is determined as having no associated structural information available no reference is made to this match in the result set. Via et al. 2008 http://structurefilter.embl.de/webservice/clients/structureFilterClient.txt
Operations
RunJob
This operation is the initial operation in a stateful interaction with the Structure Filter service.
- SOAP Action: http://structureFilter.embl.de/StructureFilter/RunJob
- Input Message: RunJobMsg
- parameters
- RunJob type
- identifier type string
- querySequence type
- restriction type string
- restriction type string
- regularExpression type
- restriction type string
- restriction type string
- elmIdentifierName type
- restriction type string
- restriction type string
- includeSecondaryStructureRecords type
- restriction type string
- restriction type string
- includeAccessibilityRecords type
- restriction type string
- restriction type string
- identifier type string
- RunJob type
- parameters
- Output Message: RunJobResponseMsg
- parameters
- RunJobResponse type
- JobIdentifier type string
- JobIdentifier type string
- RunJobResponse type
- parameters
GetStatus
This operation returns the status of a job identified by its job identifier. A client should use this operation to be aware when/if the results are available.
- SOAP Action: http://structureFilter.embl.de/StructureFilter/GetStatus
- Input Message: GetStatusMsg
- parameters
- GetStatus type
- JobIdentifier type string
- JobIdentifier type string
- GetStatus type
- parameters
- Output Message: GetStatusResponseMsg
- parameters
- GetStatusResponse type
- Status type string
- StatusDetails type string
- Status type string
- GetStatusResponse type
- parameters
- Fault Message: JobIdentifierFaultMsg
- fault
- JobIdentifierFault type
- FaultDescription type string
- FaultDescription type string
- JobIdentifierFault type
- fault
GetResult
This operation returns the resulting predictions.
- SOAP Action: http://structureFilter.embl.de/StructureFilter/GetResult
- Input Message: GetResultMsg
- parameters
- GetResult type
- JobIdentifier type string
- JobIdentifier type string
- GetResult type
- parameters
- Output Message: GetResultResponseMsg
- parameters
- GetResultResponse type
- sequence type SequenceType
- identifier type
- restriction type string
- restriction type string
- sequence type
- restriction type string
- restriction type string
- identifier type
- structureFilterRecord type StructureFilterRecordType
- ELMIdentifier type string
- regularExpression type string
- start type integer
- end type integer
- accessibilityScore type decimal
- accessibilityScorePValue type decimal
- secondaryStructureScore type decimal
- secondaryStructureScorePValue type decimal
- totalScore type decimal
- totalScorePValue type decimal
- targetDomainStructure type string
- percentageIdentity type decimal
- benchmarkAssignment type string
- individualResidueValues type IndividualResidueValuesType
- position type integer
- targetDomainStructure type string
- accessibility type decimal
- secondaryStructure type string
- position type integer
- ELMIdentifier type string
- secondaryStructureRecord type SecondaryStructureRecordType
- start type integer
- end type integer
- secondaryStructure type string
- targetDomainStructure type string
- start type integer
- accessibilityRecord type AccessibilityRecordType
- position type integer
- accessibility type decimal
- targetDomainStructure type string
- position type integer
- sequence type SequenceType
- GetResultResponse type
- parameters
- Fault Message: JobIdentifierFaultMsg
- fault
- JobIdentifierFault type
- FaultDescription type string
- FaultDescription type string
- JobIdentifierFault type
- fault
WSDL Changes
| Date | Description of Changes |
| 22nd April 2009 | First Snapshot |

Test #1: StructureFilter_test
The StructureFilter web-service consists of the following three methods:
- RunJob
- GetStatus
- GetResult
the runStructureFilterWS.py script tests the functionality of all three methods of this web-service.
The results from the Strucuture Filter web-service are deterministic so the script checks for exact values for the output.
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