Workflows

ChemFlow workflows address common computational chemistry tasks and are named with a prefix followed by “Flow”, their are: DockFlow, ScoreFlow, and LigFlow. Two additional Flows will be released soon MDFlow, HGFlow, EntropyFlow (from Pereira, G.) stay tunned for updates!

Hint

The workFlows let you harness the power of your multicore machine or HPC resource.

DockFlow

DockFlow covers docking and virtual screening of compound(s) against some single or multiple targets, with one or multiple compounds through the so far implemented docking software: Autodock Vina and PLANTS.

ScoreFlow

ScoreFlow handles the (re)scoring of complexes (such as docking poses),Structural Interaction fingerprints (using IChem), VinaSF, ChemPLP, PLP, MM/GBSA. (with or without MD, implicit/explicit solvent).

LigFlow

LigFlow handles the curation of compound libraries, stored as SMILES or MOL2 files, automating 3D conformer generation, compound parameterization and charge calculation. It also probes the ChemBase to avoid redundancy.

MDFlow (unreleased)

Handles molecular dynamics simulation protocols and analysis.

HGFlow (unreleased)

A full fledged workflow designed for Host-Guest systems such as molecular cages.

Hint

DockFlow and ScoreFlow were implemented to comply with docking/scoring benchmarks. One can test new search and scoring functions and directly compare with the competition (within ReportFlow).

Note

ChemBase is the ChemFlow database for pre-calculated molecules, so far it contains a nearly 9000 drug-like compounds from the “Chimioteque Nationale du CNRS” with HF 6-31G* QM optimized geometries and assigned parameters for GAFF2. Access requires proof of “Chimioteque” licence.