Icon

Model building on a template 1

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 Template structureKeep only the first command toedit the alignment interactively[File > Send back to KNIME]Seqconvert Disabled 29452QuerysequenceSplit complexes SiteMap Extract Properties A single bindingsite region Table Viewer Transpose Column Rename Joiner (deprecated) Prime BuildHomology Model Java EditVariable (simple) Molecule-to-MAE PDB Reader MultipleSequence Viewer ChemistryExternal Tool Concatenate Testing Internal testing 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 Template structureKeep only the first command toedit the alignment interactively[File > Send back to KNIME]Seqconvert Disabled 29452QuerysequenceSplit complexes SiteMap Extract Properties A single bindingsite region Table Viewer Transpose Column Rename Joiner (deprecated) Prime BuildHomology Model Java EditVariable (simple) Molecule-to-MAE PDB Reader MultipleSequence Viewer ChemistryExternal Tool Concatenate Testing Internal testing Sequence Reader

Nodes

Extensions

Links

Download

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

Download Workflow
On NodePit since: 2021-02-17
Last update: 2024-12-17
Created with KNIME version: v4.7.1
Tags: Real WorldPrimeGlideSiteMapPyMOLBinding SiteHomology ModelingGrid GenerationSchrodinger

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

Try NodePit Runner!