Icon

Protein patch analysis

Performes the protein patch analysis of a prepared protein structure (protein_patch_calculation.py).

Protein patch analysis:Performes the protein patch analysis of a prepared protein structure (protein_patch_calculation.py). Input(s): Protein structure as PDB-ID or MAE.Output(s):List of the calculated descriptors, written to the specified folder. Creates subdirectory for every protein entry Alternative setup that loads MAE file and createssubdirectory based on entry title. ProteinPrep canbe skipped if structres are already prepared.This example only uses one structure and onlyprocesses one type of output. by PDB process structures-treat disulfides-delete watersprotein_patch_calculation.py-FROM pspProperties only %file%to PathPDB-IDcreate pathby PDBby PDB Script optionsprotein_patch_calculation.pycreate pathPDB-IDto Path %file%PDB-IDcreate pathto Path %file%add PDB namePDB onlyadd PDB nameNode 15309process structures-treat disulfides-delete waterstitleprotein_patch_calculation.py-FROM pspby title Properties onlytitlecreate pathto Path %file%Node 15324select folderreaplce "\" on Windowsselect folderreaplce "\" on Windows Group Loop Start Get PDB Molecule-to-MAE Protein PreparationWizard ChemistryExternal Tool Column Filter Postprocessing Postprocessing Postprocessing CSV Writer Variable Loop End String to Path(Variable) Table Rowto Variable String Manipulation(Variable) Group Loop Start Group Loop Start Table Viewer Get Help String Manipulation(Variable) Table Rowto Variable Variable Loop End String to Path(Variable) CSV Writer Table Rowto Variable String Manipulation(Variable) String to Path(Variable) Variable Loop End CSV Writer Column Appender Column Filter Column Appender Molecule Reader(to MAE) Protein PreparationWizard Extract Properties ChemistryExternal Tool Group Loop Start Postprocessing Column Filter Table Rowto Variable String Manipulation(Variable) String to Path(Variable) CSV Writer Variable Loop End Concatenate Local File BrowserConfiguration String Manipulation(Variable) Local File BrowserConfiguration String Manipulation(Variable) Protein patch analysis:Performes the protein patch analysis of a prepared protein structure (protein_patch_calculation.py). Input(s): Protein structure as PDB-ID or MAE.Output(s):List of the calculated descriptors, written to the specified folder. Creates subdirectory for every protein entry Alternative setup that loads MAE file and createssubdirectory based on entry title. ProteinPrep canbe skipped if structres are already prepared.This example only uses one structure and onlyprocesses one type of output. by PDB process structures-treat disulfides-delete watersprotein_patch_calculation.py-FROM pspProperties only %file%to PathPDB-IDcreate pathby PDBby PDB Script optionsprotein_patch_calculation.pycreate pathPDB-IDto Path %file%PDB-IDcreate pathto Path %file%add PDB namePDB onlyadd PDB nameNode 15309process structures-treat disulfides-delete waterstitleprotein_patch_calculation.py-FROM pspby title Properties onlytitlecreate pathto Path %file%Node 15324select folderreaplce "\" on Windowsselect folderreaplce "\" on Windows Group Loop Start Get PDB Molecule-to-MAE Protein PreparationWizard ChemistryExternal Tool Column Filter Postprocessing Postprocessing Postprocessing CSV Writer Variable Loop End String to Path(Variable) Table Rowto Variable String Manipulation(Variable) Group Loop Start Group Loop Start Table Viewer Get Help String Manipulation(Variable) Table Rowto Variable Variable Loop End String to Path(Variable) CSV Writer Table Rowto Variable String Manipulation(Variable) String to Path(Variable) Variable Loop End CSV Writer Column Appender Column Filter Column Appender Molecule Reader(to MAE) Protein PreparationWizard Extract Properties ChemistryExternal Tool Group Loop Start Postprocessing Column Filter Table Rowto Variable String Manipulation(Variable) String to Path(Variable) CSV Writer Variable Loop End Concatenate Local File BrowserConfiguration String Manipulation(Variable) Local File BrowserConfiguration String Manipulation(Variable)

Nodes

Extensions

Links

Download

To use this workflow in KNIME, download it from the below URL and open it in KNIME:

Download Workflow
Created by: kuppurar
Created at: 2017-10-16
On NodePit since: 2023-04-21
Last update: 2024-11-21
Created with KNIME version: v4.4.1
Tags: ProteinBioluminate

Deploy, schedule, execute, and monitor your KNIME workflows locally, in the cloud or on-premises – with our brand new NodePit Runner.

Try NodePit Runner!