Python script 1-2
The Python Script nodes are used to extract ring properties, run a Macromodel conformational search with specific parameters, and measure distances between […]
MM Conformational search 1-4
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
01_Chemistry external tool
The Chemistry external tool nodes can be used to parse a log file with basic shell commands or run any command line utilities. Quick form nodes can be used […]
Cocrystallized ligand redocking 2
Extract ligands from a set of PDB protein-ligand complexes. The complexes are then prepared and a Glide grid is generated. Finally, the cocrystallized […]
AutoQSAR
Generate QSAR models for a chosen property of a set of compounds, and apply the QSAR nodel to other compounds, with either traditional QSAR methods or […]
Grid generation 1-3
Align the binding site, and prepare PDB structures, generate the Glide grids and write them to disk. Analyze the protein-ligand complex composition and […]
Protein Alignment
Extract one monomer from each of the two multimers. Align the binding sites (via the 'Align Binding Sites' node) or the whole structure (using the 'Protein […]
Build antibody 1
Several antibody models are built using Bioluminate starting from the heavy and light chain sequences. Sequences can be read from an XLS spreadsheet. […]
R group enumeration
Create libraries by substituting one or several attachments on a core structure with fragments from reagent compounds. Unique identifiers are assigned to […]
Binding Pose Metadynamics
Various binding configurations of a single ligand in a single binding site are ranked.