Database analysis 1
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 […]
Run PyMOL 1
Display structure in PyMOL. Run PyMOL commands and save the modified structures. Raytrace views and save the images. [Requires: Maestro, PyMOL] […]
Semiempirical
Run semi-empirical NDDO quantum chemical optimization and generate surface properties [Requires: Maestro, LigPrep]
FEP analysis 2
An overview (predictions along with the ligand 2D structures) of a set of single edge FEP calculations is given as well as analysis details (including […]
Node MSV
[Version: 2.9.0] [Requires: Maestro]
Batch execution 1
Test running the current workflow with KNIME_batch.py.
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 […]
Installation test
Installation check in LiveDesign Basic test and installation checking The workflow is exported as Computational model in LiveDesign. TAGS: LiveDesign
Virtual screening 1-2
Structure-based Virtual Screening Workflow incorporating ligand preparation, property filtering, and successive docking using different Glide modes (HTVS, […]
Sitemap and docking
Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each site and used to dock […]