Related PDB structures
Related PDB structures PDB structures containing ligands similar to each LiveReport structures are listed. The PDB structure with the most similar ligand […]
Clustering 1-3
Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of […]
Run PyMOL 1-2
Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]
Batch execution 2
Test running the current workflow with KNIME_batch.py.
Bioluminate 1
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 […]
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 […]
Shape screening 1-2
Use a co-crystallized ligand conformation as a query to screen a set of ligands based on the shape. Screen against several queries. Commands to run the […]
Ligand alignment
Ligand alignment in LiveDesign Ligand alignment on a template structure using Shape screening. The workflow is exported as Computational model in […]
MD simulation 1-3
Prepare a system and run a Desmond MD simulation. Individual frames are then extracted and analyzed in terms of hydrogen bond network and atom […]