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Protein model building

Protein model building on an edited alignment

Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid is generated and the binding site is analyzed. A raytrace image of the model is also created.

[Requires: Prime, Glide, SiteMap, PyMOL] [Keywords: binding site, homology modeling, grid generation]

Protein model building on an edited alignment:Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid isgenerated and the binding site is analyzed. A raytrace image of the model is also created.[Requires: Prime, Glide, SiteMap, PyMOL] [Keywords: binding site, homology modeling, grid generation]Protein and largest ligandSingle bindingsite regionSitemap terms[configure]Proteinsand ligandsLigand binding sitecharacterization Template Parameter flow variables--template-filefrom a column Save Grids Raytracingmygrid.zip Inspect the binding sitesTemplate structure Edit the alignment interactively[File > Send back to KNIME]Seqconvert QuerysequenceSplit complexes SiteMap Extract Properties A single bindingsite region Table Viewer Transpose Column Rename Joiner Prime BuildHomology Model Java EditVariable (simple) Molecule-to-MAE Glide GridGeneration Run PyMOL Glide Grid Writer Run Maestro Image to Report PDB Reader Load image MultipleSequence Viewer ChemistryExternal Tool Concatenate (Optionalin) (deprecated) Sequence Reader Protein model building on an edited alignment:Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid isgenerated and the binding site is analyzed. A raytrace image of the model is also created.[Requires: Prime, Glide, SiteMap, PyMOL] [Keywords: binding site, homology modeling, grid generation]Protein and largest ligandSingle bindingsite regionSitemap terms[configure]Proteinsand ligandsLigand binding sitecharacterization Template Parameter flow variables--template-filefrom a column Save Grids Raytracingmygrid.zip Inspect the binding sitesTemplate structure Edit the alignment interactively[File > Send back to KNIME]Seqconvert QuerysequenceSplit complexes SiteMap Extract Properties A single bindingsite region Table Viewer Transpose Column Rename Joiner Prime BuildHomology Model Java EditVariable (simple) Molecule-to-MAE Glide GridGeneration Run PyMOL Glide Grid Writer Run Maestro Image to Report PDB Reader Load image MultipleSequence Viewer ChemistryExternal Tool Concatenate (Optionalin) (deprecated) Sequence Reader

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

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On NodePit since: 2020-02-17
Last update: 2020-02-26
Created with KNIME version: v4.1.0
Tags: Real WorldPrimeGlideSiteMapPyMOLBinding SiteHomology ModelingGrid Generation

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