Icon

Model building 1-3

Protein Model Building

Read an amino acid sequence, search for possible templates, look for relevant ones, build a homology model including the largest ligand and compare it to the template structure. Run a side chain sampling and a minimization of the binding site.

Model Building: Read an amino acid sequence, search for possible templates, look for relevant ones, build a homology model including the largest ligand and compare it to the template structure. Run aside chain sampling and a minimization of the binding site.[Requires: Prime]Including the ligandSearch the pdb sequence databaseInspect the possible template list and choose one (hilite) Chosen templateFormat the listStructure contentLargest ligandCompare with the original structureAround the ligandAround the ligandASLCompare the homology model and the templateRenderingIf there is a ligandGet and prepareTemplate structure(first one by default) %file%%file%Read a FASTA sequencePrime typeExtended sampling of a loop close to the ligandCompare with the initial conformation%file%29452 Prime BuildHomology Model BLAST Table Viewer HiLite Row Splitter Table Viewer Run Maestro Prime Minimization Prime SideChain Sampling Table Row to Variable(deprecated) Concatenate Run Maestro Molecule Writer(from MAE) Molecule Writer(from MAE) Sequence Reader Java EditVariable (simple) Prime Refine Loops Run Maestro Concatenate Molecule Writer(from MAE) Test in batch Model Building: Read an amino acid sequence, search for possible templates, look for relevant ones, build a homology model including the largest ligand and compare it to the template structure. Run aside chain sampling and a minimization of the binding site.[Requires: Prime]Including the ligandSearch the pdb sequence databaseInspect the possible template list and choose one (hilite) Chosen templateFormat the listStructure contentLargest ligandCompare with the original structureAround the ligandAround the ligandASLCompare the homology model and the templateRenderingIf there is a ligandGet and prepareTemplate structure(first one by default) %file%%file%Read a FASTA sequencePrime typeExtended sampling of a loop close to the ligandCompare with the initial conformation%file%29452 Prime BuildHomology Model BLAST Table Viewer HiLite Row Splitter Table Viewer Run Maestro Prime Minimization Prime SideChain Sampling Table Row to Variable(deprecated) Concatenate Run Maestro Molecule Writer(from MAE) Molecule Writer(from MAE) Sequence Reader Java EditVariable (simple) Prime Refine Loops Run Maestro Concatenate Molecule Writer(from MAE) Test in batch

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: 2020-08-12
Last update: 2024-12-17
Created with KNIME version: v4.3.2
Tags: Prime

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

Try NodePit Runner!