Icon

Bioluminate 1-4

BioLuminate Residue Scanning

The antibody structure can be split into Fc, Fab and Fv domains. The node scans proteins for residues that are candidates for mutation and evaluate the stability and affinity of the mutated structures. Additionally, you can gain access to the latest command-line only functionalities of the tool (e.g., to control Prime loop sampling options), run affinity maturation and aggregation calculations that can be used to compare the mutants.

[Requires: Bioluminate]

BioLuminate Residue Scanning: The antibody structure can be split into Fc, Fab and Fv domains. The node scans proteins for residues that are candidates for mutation and evaluate the stabilityand affinity of the mutated structures. Additionally, you can gain access to the latest command-line only functionalities of the tool (e.g., to control Prime loopsampling options), run affinity maturation and aggregation calculations that can be used to compare the mutants.[Requires: Bioluminate]SeqconvertExtract the sequence [configurable] Mutated structuresAntibody/Antigen complexKeep chains H,L,WBioluminate profileCartoon ribbons colored by antibody structureAll - A(ction) > Preset > AntibodyLists of mutations Antibody structure split into Fc, Fab and Fv Fast minimization(see the help message)Mutations H:103-105including affinity Mutations H:103-105Bioluminate Delta Affinity and stability Mutants with several mutationsAffinity and stabilityMutants with several mutationsStability only BioluminateBioluminate Delta Affinity and stability Delta stability Similar sequences Similar sequences Mutated structures [configurable]Prime loop refinement(time consuming calculation) Command line optionsSplit antibodyRegions Similar structureAligned by residue numberin the sequence viewer on multiple structures Mutations H:103-105Keep chain HBioluminate Delta stabilityfor several structures [configurable] Running calculationSubjobsCalculation status ChemistryExternal Tool Rendering Run Maestro Get PDB Protein PreparationWizard Delete Atoms Run Maestro Table Creator Chunk Loop Start Ungroup MAE Run Maestro Cross Joiner Java EditVariable (simple) Residue Scanning Loop End(deprecated) Residue Scanning Extract Properties Table Viewer Several mutations Residue Scanning Several mutations Residue Scanning Chunk Loop Start Loop End(deprecated) Extract Properties Extract Properties Table Viewer Table Viewer Column Resorter Postprocessing Postprocessing BLAST Table Viewer Postprocessing Run Maestro Prime loopprediction Table Viewer ChemistryExternal Tool Table Viewer Ungroup MAE Extract Properties Get PDB Protein PreparationWizard Run Maestro Residue Scanning Ungroup MAE Residue Scanning Delete Atoms Extract Properties Ungroup MAE Table Viewer Column Resorter Rendering Get Help Job Control Job Control Table Viewer Concatenate Concatenate BioLuminate Residue Scanning: The antibody structure can be split into Fc, Fab and Fv domains. The node scans proteins for residues that are candidates for mutation and evaluate the stabilityand affinity of the mutated structures. Additionally, you can gain access to the latest command-line only functionalities of the tool (e.g., to control Prime loopsampling options), run affinity maturation and aggregation calculations that can be used to compare the mutants.[Requires: Bioluminate]SeqconvertExtract the sequence [configurable] Mutated structuresAntibody/Antigen complexKeep chains H,L,WBioluminate profileCartoon ribbons colored by antibody structureAll - A(ction) > Preset > AntibodyLists of mutations Antibody structure split into Fc, Fab and Fv Fast minimization(see the help message)Mutations H:103-105including affinity Mutations H:103-105Bioluminate Delta Affinity and stability Mutants with several mutationsAffinity and stabilityMutants with several mutationsStability only BioluminateBioluminate Delta Affinity and stability Delta stability Similar sequences Similar sequences Mutated structures [configurable]Prime loop refinement(time consuming calculation) Command line optionsSplit antibodyRegions Similar structureAligned by residue numberin the sequence viewer on multiple structures Mutations H:103-105Keep chain HBioluminate Delta stabilityfor several structures [configurable] Running calculationSubjobsCalculation status ChemistryExternal Tool Rendering Run Maestro Get PDB Protein PreparationWizard Delete Atoms Run Maestro Table Creator Chunk Loop Start Ungroup MAE Run Maestro Cross Joiner Java EditVariable (simple) Residue Scanning Loop End(deprecated) Residue Scanning Extract Properties Table Viewer Several mutations Residue Scanning Several mutations Residue Scanning Chunk Loop Start Loop End(deprecated) Extract Properties Extract Properties Table Viewer Table Viewer Column Resorter Postprocessing Postprocessing BLAST Table Viewer Postprocessing Run Maestro Prime loopprediction Table Viewer ChemistryExternal Tool Table Viewer Ungroup MAE Extract Properties Get PDB Protein PreparationWizard Run Maestro Residue Scanning Ungroup MAE Residue Scanning Delete Atoms Extract Properties Ungroup MAE Table Viewer Column Resorter Rendering Get Help Job Control Job Control Table Viewer Concatenate Concatenate

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: jcmozzic
Created at: 2013-09-17
On NodePit since: 2020-08-12
Last update: 2024-11-18
Created with KNIME version: v4.5.1
Tags: ProteinBioluminateSchrodinger

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

Try NodePit Runner!