MolSanitizer: An open-source pipeline to prepare small-molecule databases for large-scale virtual screening
Year: 2026
Type: preprint
Abstract: Accurate preparation of small-molecule databases for virtual screening is crucial for the success of computer-aided drug discovery. Although numerous free software options are available, they often underperform compared to commercial alternatives. Here, we introduce MolSanitizer, an open-source molecular preparation pipeline built on RDKit and designed for large-scale virtual screening. MolSanitizer extends existing open-source functionality through curated, chemical-environment-aware rules for protonation and tautomerization, systematic stereoisomer enumeration, and a dedicated conformer generator that combines knowledge-based structural preferences with stochastic torsional sampling. Our benchmarking results show that MolSanitizer achieves better performance than several free software alternatives while achieving performance levels comparable to commercial software. MolSanitizer features a modular and open-source design, allowing users to easily customize the tool to meet their specific needs. MolSanitizer also generates output files compatible with several widely used molecular docking programs, thereby facilitating a streamlined workflow for users. MolSanitizer is available for free at https://github.com/carlssonlab/MolSanitizer and via a web server at https://carlssonlabtools.icm.uu.se/molsani.
Source: ChemRxiv
Language: English
Subfield: Drug Discovery
Domain: Life Sciences
Open Access status: green
Awards: G1441096865, G3344207039, G3631573628, G429838583, Ultra-rapid lead generation for antiviral drug discovery: Structure-based design of dengue virus inhibitors, G4632909464, G5404377299, Molecular control of dopaminergic signaling by allosteric modulators and designer receptors, G796431723, NAISS
OpenAlex ID: W7221087724