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Workflows
Examples which show capabilities of 3D-e-Chem Knime nodes can be found in the default Knime workspace (/home/vagrant/knime-workspace) inside the 3D-e-Chem-Examples folder.
Workflows which have been made to produce scientific results in the project. The workflows can be found in the default Knime workspace (/home/vagrant/knime-workspace) inside the 3D-e-Chem Workflows folder.
The Pymol session files (*.pse) can by opened with PyMol.
The workflows are available on Github at https://github.com/3D-e-Chem/workflows
Customizable KNIME workflow to extract GPCR ligands from ChEMBL and preparation for virtual screening.
Workflow to analyze the binding site similarity between all crystallized GPCRs and kinases. PDB IDs are fetched through GPCRdb and KLIFS nodes, and the KRIPO nodes are used to select similar binding pockets and to add ligand structures.
A Pymol session file called 'GPCR-kinase.pse' is stored next to this workflow.
This example fetches the residues, structures, protein-ligand interactions, and mutations of the human beta-2 adrenoreceptor and its similarity to other beta-2 adrenoreceptors.
Data is fetched from http://gpcrdb.org website.
A Pymol session file called aminergic_alignment.pse with an aminergic alignment is stored next to this workflow.
Example for KLIFS nodes
This example performs interaction fingerprint analysis of human MAPK-ligand complexes.
Data is fetched from http://klifs.vu-compmedchem.nl/
Bioisosteric replacement workflow using Kripo Knime nodes.
A Pymol session file called KRIPO_3rze_2aot.pse with 3rze + 2aot Kripo fragment alignment is stored next to this workflow.