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Model building on a template 1-2

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]Single bindingsite regionSitemap termsLigand 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 Querysequence[configure]Proteinsand ligandsProtein and largest ligandSiteMap Extract Properties Table Viewer Transpose Column Rename Joiner (deprecated) 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 A single bindingsite region Split complexes 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]Single bindingsite regionSitemap termsLigand 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 Querysequence[configure]Proteinsand ligandsProtein and largest ligandSiteMap Extract Properties Table Viewer Transpose Column Rename Joiner (deprecated) 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 A single bindingsite region Split complexes

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On NodePit since: 2021-02-17
Last update: 2026-01-07
Created with KNIME version: v4.7.1
Tags: Real WorldPrimeGlideSiteMapPyMOLBinding SiteHomology ModelingGrid GenerationSchrodinger

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