Web Service wiws SOAP Nl

aka WHAT IF web services Add_annotation_inactiveAdd_annotation_inactiveLog in to add alternative_name
WARNING
Annotations: 201 Total number of annotations from the provider's definition / description document. 193 Total number of annotations submitted by members of BioCatalogue. 8 Total number of annotations sourced from other registries. 0

SOAP Operations (100)

These are the SOAP operations available for the SOAP variant of this service. Click on each one to get more information and to annotate.
Quick Browse | AtomAccessibilityMolecular | AtomAccessibilityMolecularPlus | AtomAccessibilitySolvent | AtomAccessibilitySolventPlus | CorrectedPDBasXML | CysteineTorsions | DownloadPDB | EchoPDB | GetSurfaceDots | HappyValue | HasHydrogenBonds | HasHydrogenBondsNoWater | HasMetalContacts | HasMetalContactsPlus | HasMultimerContacts | HasNegativeIonContacts | HasNegativeIonContactsPlus | HasNucleicContacts | HasSaltBridge | HasSaltBridgePlus | HETGroupNames | ImproperQualityMax | ImproperQualitySum | InsideOutsideDistribution | ListContactsNormal | ListContactsRelaxed | ListSideChainContactsNormal | ListSideChainContactsRelaxed | MovedWaterPDB | MovedWaterPDBasXML | MutationBumps | NPF_Free_Metal_Contact_Value | NPF_HappyValue | NPF_HappyValueX | NPF_HasMultimerContacts | NPF_Ligand_Contact_Value | NPF_Metal_Contact_Value | NPF_Neg_Ion_Contact_Value | NPF_ProlineMutationValue | NPF_SaltBridges | NPF_ShowBumps | NPF_SymmetryContact | PackingQuality | PackingQualityMolecule | PDBasXML | PDBasXMLorg | PDBasXMLwithPolarH | PDBasXMLwithSymwithPolarH | PDB_sequence | ProfileHSSP | ProlineMutationValue | ProlineMutationValueRange | ReadAtom | ReadCoordinate | ReadDot | ReadMoleculeValue | ReadProfileEntry | ReadResidue | ResidueAccessibilityMolecular | ResidueAccessibilitySolvent | ResidueAccessibilityVacuum | ResidueAccessibilityVacuumMolecular | ResidueBfactors | ResidueDSSP | ResidueDSSPplusLocal | ResidueToFullResidue | ResidueTorsions | ResidueTorsionsBB | ShowAccessAndSymmetry | ShowBumps | ShowCysteineBridge | ShowCysteineBridgeNoPisa | ShowCysteineFree | ShowCysteineMetal | ShowDrugContacts | ShowDrugContactsShort | ShowHydrogenBonds | ShowHydrogenBondsM | ShowLigandContacts | ShowLikelyRotamers | ShowProteiNucleicContacts | ShowSaltBridges | ShowSaltBridgesH | ShowTauAngle | SymmetryContact | SymmetryContactSide | SymmetryContactTot | SymShellFiveXML | SymShellOneXML | SymShellTenXML | SymShellTwoXML | TestEmpty | TotAccessibilityMolecular | TotAccessibilitySolvent | UploadPDB | UseFileDB | UseResidueDB | VariabilityHSSP | WouterHack | WouterHack2 |

AtomAccessibilityMolecular

1 input | 1 output

Part of Service: wiws

command: WSVACM description: Returns for each atom in the input file its accessibile molecular surface in Ångström2. Waters a...
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AtomAccessibilityMolecularPlus

1 input | 1 output

Part of Service: wiws

command: WSVAMP description: Returns for each atom in the input file its accessibile molecular surface in Ångström2. Waters a...
Tags on this SOAP Operation:
none

AtomAccessibilitySolvent

1 input | 1 output

Part of Service: wiws

command: WSVACC description: Returns for each atom in the input file its solvent accessibility in Ångström2. Waters are negle...
Tags on this SOAP Operation:
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AtomAccessibilitySolventPlus

1 input | 1 output

Part of Service: wiws

command: WSVACP description: Returns for each atom in the input file its solvent accessibility in Ångström2. Waters are negle...
Tags on this SOAP Operation:
none

CorrectedPDBasXML

1 input | 1 output

Part of Service: wiws

command: WSVCOA description: Before returning the coordinates in XML format, WHAT IF applies a series of small `corrections`:
  1. Alternate at...
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none

CysteineTorsions

1 input | 1 output

Part of Service: wiws

command: WSVCYT description: Returns for each cysteine (bridge) all its torsion angles (in degrees).
These are the torsion angles over the foll...
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none

DownloadPDB

1 input | 1 output

Part of Service: wiws

command: na description: You can use this function to download PDB files. If you use the regular four letter code, you can retrieve standard PDB fi...
Tags on this SOAP Operation:
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EchoPDB

1 input | 1 output

Part of Service: wiws

command: WSVECH description: This service returns the PDB file that you upload in PDB format. Most HEADERcards are skipped, so are ANISOU cards, an...
Tags on this SOAP Operation:
none

GetSurfaceDots

1 input | 1 output

Part of Service: wiws

command: WSVDOT description:

Graphics

Calculates the positions of dots that are homogeneously distributed over the surface of the molecule ...
Tags on this SOAP Operation:
none

HappyValue

1 input | 1 output

Part of Service: wiws

command: WSVHAP description: This service determines for each position the molecule that is further than two positions away from a terminus a score...
Tags on this SOAP Operation:
none

HasHydrogenBonds

1 input | 1 output

Part of Service: wiws

command: WSVHBF description: For each amino acid in the input file the H-bond enthalpy is calculated for each side chain atom. All these enthalpies...
Tags on this SOAP Operation:
none

HasHydrogenBondsNoWater

1 input | 1 output

Part of Service: wiws

command: WSVHBN description: For each amino acid in the input file the H-bond enthalpy is calculated for each side chain atom. All these enthalpies...
Tags on this SOAP Operation:
none

HasMetalContacts

1 input | 1 output

Part of Service: wiws

command: WSVHIC description: For each amino acid in the input file the ion contacts are counted. Depending on the distance they get a score ranging...
Tags on this SOAP Operation:
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HasMetalContactsPlus

1 input | 1 output

Part of Service: wiws

command: WSLHIC description: For each amino acid in the input file the ion contacts are counted. Depending on the distance they get a score ranging...
Tags on this SOAP Operation:
none

HasMultimerContacts

1 input | 1 output

Part of Service: wiws

command: WSVANP description: For each amino acid in the input file the contacts with other protein chains in the multimer are counted. This is a si...
Tags on this SOAP Operation:
none

HasNegativeIonContacts

1 input | 1 output

Part of Service: wiws

command: WSVHIN description: For each amino acid in the input file the ion contacts are counted. Depending on the distance they get a score ranging...
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HasNegativeIonContactsPlus

1 input | 1 output

Part of Service: wiws

command: WSLHIN description: For each amino acid in the input file the ion contacts are counted. Depending on the distance they get a score ranging...
Tags on this SOAP Operation:
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HasNucleicContacts

1 input | 1 output

Part of Service: wiws

command: WSVHDC description: For each amino acid in the input file the contacts with nucleic acids are counted. This is a simple count, and has no ...
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none

HasSaltBridge

1 input | 1 output

Part of Service: wiws

command: WSVHSB description: For each amino acid in the input file its side chain salt bridges are counted, valued, and added up. The total quasi s...
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HasSaltBridgePlus

1 input | 1 output

Part of Service: wiws

command: WSLHSB description: For each amino acid in the input file its side chain salt bridges are counted, valued, and added up. The total quasi s...
Tags on this SOAP Operation:
none

HETGroupNames

1 input | 1 output

Part of Service: wiws

command: WSVHET description: The PDB has, for obscure reasons, decided to have atoms and hetatoms. Ligands, lipids, and ions tend to become hetatom...
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ImproperQualityMax

1 input | 1 output

Part of Service: wiws

command: WSVCHX description: Returns for each residue the maximum of all its improper dihedral Z-scores.

Typical X-ray things

summary: I...
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ImproperQualitySum

1 input | 1 output

Part of Service: wiws

command: WSVCHN description: Returns for each residue the sum of all improper dihedral Z-scores observable in that residue. One thus expects larger...
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InsideOutsideDistribution

1 input | 1 output

Part of Service: wiws

command: WSVINO description: Returns an inside - outside normality score that is callibrated against PDB files ofwater-soluble molecules. One score...
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ListContactsNormal

1 input | 1 output

Part of Service: wiws

command: WSLCON description: For each amino acid its atomic contacts are counted with everything but water. All distances are scored using a way to...
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ListContactsRelaxed

1 input | 1 output

Part of Service: wiws

command: WSLCNR description: For each amino acid its atomic contacts are counted with everything but water. All distances are scored using a way to...
Tags on this SOAP Operation:
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ListSideChainContactsNormal

1 input | 1 output

Part of Service: wiws

command: WSLCN2 description: For each amino acid its side chain contacts (excluding Cβ) are counted with everything but water. All distances a...
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ListSideChainContactsRelaxed

1 input | 1 output

Part of Service: wiws

command: WSLCN3 description: For each amino acid its side chain contacts (excluding Cβ) are counted with everything but water. All distances a...
Tags on this SOAP Operation:
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MovedWaterPDB

1 input | 1 output

Part of Service: wiws

command: WSVMWA description: For a crystallographer, a position in the "next cell" is just as good as a position in the cell where all th...
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MovedWaterPDBasXML

1 input | 1 output

Part of Service: wiws

command: WSVMWX description: For a crystallographer, a position in the "next cell" is just as good as a position in the cell where all th...
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MutationBumps

1 input | 1 output

Part of Service: wiws

command: WSVMBA description: Returns for each residue in the mutated protein the integrated bump value after optimally executing the mutatation. Tw...
Tags on this SOAP Operation:
none

NPF_Free_Metal_Contact_Value

1 input | 1 output

Part of Service: wiws

command: NPFHC4 description: Determines contacts of all atoms in a residue with free metals and gives those a score.So a contact with iron in a hem...
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NPF_HappyValue

1 input | 1 output

Part of Service: wiws

command: NPFPRO description: This service determines for each amino acid (that is further than two positions away from a terminus) a score that rel...
Tags on this SOAP Operation:
none

NPF_HappyValueX

1 input | 1 output

Part of Service: wiws

command: NPFHAP description: This service determines for each amino acid (that is further than two positions away from a terminus) a score that rel...
Tags on this SOAP Operation:
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NPF_HasMultimerContacts

1 input | 1 output

Part of Service: wiws

command: NPFANP description: For each amino acid the contacts with other protein chains in the multimer are counted. This is a simple count, and ha...
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NPF_Ligand_Contact_Value

1 input | 1 output

Part of Service: wiws

command: NPFHC2 description: Determines contacts of all atoms in a residue with a ligand and gives those a score.These scores are only vaguely rela...
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NPF_Metal_Contact_Value

1 input | 1 output

Part of Service: wiws

command: NPFHC1 description: Determines contacts of all atoms in a residue with metals and gives those a score.These scores are only vaguely relate...
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NPF_Neg_Ion_Contact_Value

1 input | 1 output

Part of Service: wiws

command: NPFHC3 description: Determines contacts of all atoms in a residue with a negative ion and gives those a score.These scores are only vaguel...
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NPF_ProlineMutationValue

1 input | 1 output

Part of Service: wiws

command: NPFPRO description: This service determines for each position the molecule that is further than two positions away from a terminus a score...
Tags on this SOAP Operation:
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NPF_SaltBridges

1 input | 1 output

Part of Service: wiws

command: NPFSBR description: For each amino acid in the input file the shortest distance of any charged atom to any other (oppositely) charged atom...
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NPF_ShowBumps

1 input | 1 output

Part of Service: wiws

command: NPFBMP description: Show Interatomic bumps The output gives per residue the integrated degree of interpenetrationwith everything else. A b...
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NPF_SymmetryContact

1 input | 1 output

Part of Service: wiws

command: NPFSMC description: Returns for each residue the number of symmetry contacts made by that whole residue.
Two atoms (of which one in `...
Tags on this SOAP Operation:
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PackingQuality

1 input | 1 output

Part of Service: wiws

command: WSVQUA description: Returns for each residue is packing normality. The normal score for proteins solved correctly at high resolution is ab...
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PackingQualityMolecule

1 input | 1 output

Part of Service: wiws

command: WSVQUM description: Returns packing normality for whole entry. The normal score for proteins solved correctly at high resolution is about ...
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PDBasXML

1 input | 1 output

Part of Service: wiws

command: WSVLAT description: Lists residues in a format the PDB should actually have chosen.
The output uses the PDBXML nomenclature but a smar...
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PDBasXMLorg

1 input | 1 output

Part of Service: wiws

command: WSVLOT description: Lists residues in a format the PDB should actually have chosen.
The output uses the PDBXML nomenclature but a smar...
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PDBasXMLwithPolarH

1 input | 1 output

Part of Service: wiws

command: WSVCO2 description: The hydrogenbond optimisation routines are used to calculate optimal positions for polar protons. This module does not...
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PDBasXMLwithSymwithPolarH

1 input | 1 output

Part of Service: wiws

command: WSVCO3 description: The hydrogenbond optimisation routines are used to calculate optimal positions for polar protons. This module takes sy...
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PDB_sequence

1 input | 1 output

Part of Service: wiws

command: WSVSEQ description: The sequence in a PDB file is not uniquely defined. This server returns what WHAT IF thinks is the sequence in the PDB...
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ProfileHSSP

1 input | 1 output

Part of Service: wiws

command: WSVPRF description: Warning. This service only returns results for PDB files known by HSSP, and those are the protein-containing subset of...
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ProlineMutationValue

1 input | 1 output

Part of Service: wiws

command: WSVPRO description: This service determines for each position the molecule that is further than two positions away from a terminus a score...
Tags on this SOAP Operation:
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ProlineMutationValueRange

1 input | 1 output

Part of Service: wiws

command: WSVPRR description: This service determines for each position the given range (that is further than two positions away from any terminus) ...
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ReadAtom

1 input | 1 output

Part of Service: wiws

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ReadCoordinate

1 input | 1 output

Part of Service: wiws

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ReadDot

1 input | 1 output

Part of Service: wiws

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none

ReadMoleculeValue

1 input | 1 output

Part of Service: wiws

Tags on this SOAP Operation:
none

ReadProfileEntry

1 input | 1 output

Part of Service: wiws

Tags on this SOAP Operation:
none

ReadResidue

1 input | 1 output

Part of Service: wiws

Tags on this SOAP Operation:
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ResidueAccessibilityMolecular

1 input | 1 output

Part of Service: wiws

command: WSVAM2 description: Returns for each residue the backbone solvent accessibility, sidechain solvent accessibility, total solvent accessibil...
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ResidueAccessibilitySolvent

1 input | 1 output

Part of Service: wiws

command: WSVAR2 description: Returns for each residue the backbone molecular accessible surface, sidechain molecular accessible surface, total mole...
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none

ResidueAccessibilityVacuum

1 input | 1 output

Part of Service: wiws

command: WSVAR3 description: Returns for each residue the accessible surface, and the vacuum accessible surface. The latter is defined as the acces...
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ResidueAccessibilityVacuumMolecular

1 input | 1 output

Part of Service: wiws

command: WSVAM3 description: Returns for each residue the molecular surface, and the vacuum molecular surface. The latter is defined as the molecul...
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ResidueBfactors

1 input | 1 output

Part of Service: wiws

command: WSVBFA description: Returns per amino acid (in this order) the values :
Average B-factor of all atoms;
B-factor of the alpha carbon...
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ResidueDSSP

1 input | 1 output

Part of Service: wiws

command: WSVHST description: Returns for each residue the DSSP determined secondary structure in three-state (HSC). summary: Reduced DSSP output
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ResidueDSSPplusLocal

1 input | 1 output

Part of Service: wiws

command: WSVHSL description: Returns for each residue the DSSP determined secondary structure in three-state (HSC). It than determines (coarsly) wh...
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ResidueToFullResidue

1 input | 1 output

Part of Service: wiws

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ResidueTorsions

1 input | 1 output

Part of Service: wiws

command: WSVCHI description: Returns for each residue all its torsion angles: φ, ψ, ω, χ14 (in degree...
Tags on this SOAP Operation:
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ResidueTorsionsBB

1 input | 1 output

Part of Service: wiws

command: WSVCHB description: Returns for each residue all its backbone torsion angles: φ, ψ, ω (in degrees).
φ, ψ and &om...
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ShowAccessAndSymmetry

1 input | 1 output

Part of Service: wiws

command: WSVJOP description: Show accessibilities and symmetry contact details, decomposed in classes. Output is a list of records, each record con...
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ShowBumps

1 input | 1 output

Part of Service: wiws

command: WSVBMP description: Show Interatomic bumps The output are those pairs of atoms considered a bump, and their degree of interpenetration. A ...
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ShowCysteineBridge

1 input | 1 output

Part of Service: wiws

command: WSVCYS description: Show Cysteine bridges.
summary: Lists cysteine bridges
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ShowCysteineBridgeNoPisa

1 input | 1 output

Part of Service: wiws

command: WSVCNP description: Show Cysteine bridges, but skip those that are between Pisa generated copies.
This option was needed for one partic...
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ShowCysteineFree

1 input | 1 output

Part of Service: wiws

command: WSVCYS description: Show Cysteine bridges.
A cysteine is called free when it neither is involved in a cysteine bridge, nor functions a...
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ShowCysteineMetal

1 input | 1 output

Part of Service: wiws

command: WSVCYM description: Show cysteines that are bound to a metal.
Metals are either included when they are covalently bound to a cysteine ...
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ShowDrugContacts

1 input | 1 output

Part of Service: wiws

command: WSVLC2 description: Show drug-like ligand interactions
The output are those pairs of atoms of which one is a drug like ligand and the ...
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ShowDrugContactsShort

1 input | 1 output

Part of Service: wiws

command: WSVLC3 description: Show drug-like ligand interactions
The output lists all residues that have a contact with (at least one) a drug-li...
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ShowHydrogenBonds

1 input | 1 output

Part of Service: wiws

command: WSVHBO description: Lists potential hydrogenbonds between amino acids and anything.
The hydrogen bonding network is not optimised, and...
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ShowHydrogenBondsM

1 input | 1 output

Part of Service: wiws

command: WSVHB- description: Lists potential hydrogenbonds between amino acids and anything but water. See ShowHydrogenBonds if you want to include...
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ShowLigandContacts

1 input | 1 output

Part of Service: wiws

command: WSVLIC description: Show ligand interactions
The output are those pairs of atoms of which one is ligand and the other macromolecule, t...
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ShowLikelyRotamers

1 input | 1 output

Part of Service: wiws

command: WSVROT description: Show Rotamer likelyhoods for all 20 amino acid types at each position in the protein. Output is a list of records, eac...
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ShowProteiNucleicContacts

1 input | 1 output

Part of Service: wiws

command: WSVANU description: Show protein - nucleic acid interactions
The output are those pairs of atoms of which one is protein and the other...
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ShowSaltBridges

1 input | 1 output

Part of Service: wiws

command: WSVSBR description: Show saltbridges
The output are those pairs of atoms considered a salt-bridge, and the shortest inter-atomic dista...
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ShowSaltBridgesH

1 input | 1 output

Part of Service: wiws

command: WSVSB2 description: Show saltbridges
The output are those pairs of atoms considered a salt-bridge, and the shortest inter-atomic dista...
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ShowTauAngle

1 input | 1 output

Part of Service: wiws

command: WSVTAU description: For each canonical amino acid in the input file the backbone angle tau is listed.

Protein engineering

summa...
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SymmetryContact

1 input | 1 output

Part of Service: wiws

command: WSVSMC description: Returns for each residue the number of symmetry contacts made by that whole residue.
Two atoms (of which one in `...
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SymmetryContactSide

1 input | 1 output

Part of Service: wiws

command: WSVSMS description: Returns for each amino acid the number of symmetry contacts made by it's side chain. For glycine the Calpha is conside...
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SymmetryContactTot

1 input | 1 output

Part of Service: wiws

command: TSVSMC description: Returns for each thing the number of symmetry contacts made by that whole thing. A thing can be amino acid, nucleic ac...
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SymShellFiveXML

1 input | 1 output

Part of Service: wiws

command: WSVSS1 description: All residues that can be generated from the assymmetric unit by applying the space group symmetry matrices and whole c...
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SymShellOneXML

1 input | 1 output

Part of Service: wiws

command: WSVSS1 description:

Returning symmetry related residues

All residues that can be generated from the assymmetric unit by applyin...
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SymShellTenXML

1 input | 1 output

Part of Service: wiws

command: WSVSST description: All residues that can be generated from the assymmetric unit by applying the space group symmetry matrices and whole c...
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SymShellTwoXML

1 input | 1 output

Part of Service: wiws

command: WSVSS1 description: All residues that can be generated from the assymmetric unit by applying the space group symmetry matrices and whole c...
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none

TestEmpty

1 input | 1 output

Part of Service: wiws

command: WEMPTY description: This web-service calls all functions and routines that all WHAT IF web-services have in common, but otherwise does no...
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TotAccessibilityMolecular

1 input | 1 output

Part of Service: wiws

command: TSVAM2 description: Returns for each entity the backbone, side chain, and totalsolvent accessibility, plus a flag that is T or F. T when a...
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TotAccessibilitySolvent

1 input | 1 output

Part of Service: wiws

command: TSVAR2 description: Returns for each entity the backbone, side chain, and totalmolecular accessibility, plus a flag that is T or F. T when...
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UploadPDB

1 input | 1 output

Part of Service: wiws

command: na description: To use WHAT-IF functions on your own PDB files, you have to upload them first. The result of this function is an ID that y...
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UseFileDB

1 input | 1 output

Part of Service: wiws

command: WSVUFI description: Returns for each PDB file a series of values that tell you whether you can use this file in database applications or t...
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UseResidueDB

1 input | 1 output

Part of Service: wiws

command: WSVUDB description: Returns for each residue a value that tells you whether you can use this residue in database applications or that you ...
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none

VariabilityHSSP

1 input | 1 output

Part of Service: wiws

command: WSVVAR description: Warning. This service only returns results for PDB files known by HSSP, and those are the protein-containing subset of...
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WouterHack

1 input | 1 output

Part of Service: wiws

command: WSVWTH description: Only Wouter can use this thing... Per residue you receive the original DSSP determination (where loop and turn both ar...
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WouterHack2

1 input | 1 output

Part of Service: wiws

command: WSVWH2 description: Only Wouter should use this thing... summary: Gives the old and the cleaned secondary structure
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Archived Operations (11) Info