Workflows

This workflow performs a basic Virtual Drug Screening Pipeline. THe workflows uses the following protocols: 1.a) Import receptor: Imports the atomic structure with PDB code 4ERF. 1.b) Import small molecules: Imports a set of 4 molecules from local files. 2.a) Receptor preparation: selects A chain and cleans the structure from waters and heteroatoms 2.b) RDKit Molecules preparation: adds hydrogens and prepares the molecules for docking 3.a) Find pockets: uses P2Rank to predict the most promising ...

This workflows contains a pipeline in Scipion that performs the following steps:

1. Import atomic structure: introduces a protein atomic structure in the pipeline as receptor.

2. Receptor preparation: uses bioPython to prepare the receptor structure, removing waters, adding hydrogens and removing unnecessary chains if asked. Also, uses PDBFixer to optimize the structure if selected.

3. Protein pocket search: uses 3 different software (P2Rank, AutoSite and FPocket) for predicting the receptor ...

This workflows contains a pipeline in Scipion that performs the following steps:

1.1) Import small molecules: introduces a set of small molecular structures in the pipeline as prospective ligands

1.2) Import atomic structure: introduces a protein atomic structure in the pipeline as receptor.

2.1) Ligand preparation: uses RDKit to prepare the small molecules optimizing their 3D structure.

2.2) Receptor preparation: uses bioPython to prepare the receptor structure, removing waters, adding hydrogens ...