Reactive protein residues
Reactive protein residues are listed and compared for a set of structures. They are also highlighted when inspecting the structures. [Requires: […]
Watermap 2
A Watermap job is submitted and the map inspected in Maestro. It could be run on several complexes in one run.
Protein model building
Use the Multiple Sequence Viewer to edit an alignment and a corresponding homology model is built. A Glide grid is generated and the binding site is […]
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 […]
Bioluminate 1-3
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 […]
Tools
Extract the atom-level properties to list the PDB conversion problems. [Requires: -] See other workflow examples using the Extract atom/bond […]
MM Conformational search 1-2
Extract ligands from PDB structures and run ConfGen. Compare the conformations in terms of RMSD and intramolecular distance. Extract conformer cluster […]
QM Conformational search 1-2
Conformers generated with MacroModel are refined with Jaguar. They are then compared in terms of geometry and Boltzmann populations. A KNIME Report designer […]
Compare confo search methods
Run a conformational search with various methods and compare the lowest energy conformers. Parse the log file to extract relevant information. [Requires: […]