Database analysis 1-2
Assess the coverage of a database from the distribution of the distance to the nearest neighbor of each molecule in the database. List the three most […]
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 […]
Jobcontrol 1
The Jobcontrol node can be used to list the currently and recently run jobs, display information on these jobs, list and inspect the corresponding files. It […]
Clustering 1
Cluster structures by fingerprints and inspect the clustering statistics to choose a good number of clusters. Create automatically the optimum number of […]
Parameter flow variables 1
Use the parameter flow variables to control command-line options not exposed in the configuration panel. This is illustrated for the protein preparation, […]
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 […]
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 […]
MCSS 1-3
Create all possible MCS groups and list the groups identified. Inspect the compounds in the first group and list the compounds that aren't included in this […]
GroupBy 1-2
Illustrate how to use the GroupBy node in the context of the ionization form prediction over a range of pH. Various aggregation methods are used: […]
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 […]