Macs in Chemistry

Insanely Great Science

Screenlamp:- A toolkit for ligand-based virtual screening


A recent publication "Enabling the hypothesis-driven prioritization of ligand candidates in big databases: Screenlamp and its application to GPCR inhibitor discovery for invasive species control" {DOI]( describes a very interesting software tool for virtual screening.

While the advantage of screening vast databases of molecules to cover greater molecular diversity is often mentioned, in reality, only a few studies have been published demonstrating inhibitor discovery by screening more than a million compounds for features that mimic a known three-dimensional (3D) ligand. Two factors contribute: the general difficulty of discovering potent inhibitors, and the lack of free, user-friendly software to incorporate project-specific knowledge and user hypotheses into 3D ligand-based screening. The Screenlamp modular toolkit presented here was developed with these needs in mind.

The Screenlamp homepage gives more details and installation instructions. Screenlamp is written in Python (3.6) and can be downloaded from GitHub

Certain submodules within screenlamp require external software to sample low-energy conformations of molecules and to generate pair-wise overlays. The tools that are currently being used in the pre-built, automated screening pipeline are OpenEye OMEGA and OpenEye ROCS to accomplish those tasks. However, screenlamp does not strictly require OMEGA and ROCS, and you are free to use any open source alternative that provided that the output files are compatible with screenlamp tools, which uses the MOL2 file format.

Screenlamp is research software and has been made available to other researchers under a permissive Apache v2 open source license.

blog comments powered by Disqus