Whilst there are a number of proprietary applications for virtual screening there are few open-source alternatives. Whilst most of the functionality needed is available in cheminformatics toolkits it is a challenge for non-coders to build the workflow needed.
VSFlow is an open-source command-line tool built on top of the RDKit for the ligand-based virtual screening of large compound libraries (databases). It includes a substructure-based, a fingerprint-based and a shape-based virtual screening tool.
Now Healx have developed Lig3DLens an end-to-end computational toolbox for 3D virtual screening based on the shape and electrostatics similarity to a reference (hit) compound. A drug designer can use a reference molecule and a (commercial) compound library of interest as inputs. The final output is a set of chemically diverse compounds with high 3D similarity to the reference compound.
Lig3DLens uses RDKit to generate the 3D conformers of the library compounds and align them to the reference compound and uses the ESPSim package to include an electrostatics term in the 3D scoring function.
All the code is on GitHub https://github.com/healx/lig3dlens and can be installed using PIP
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python -m pip install -r requirements.txt |