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PreprintCC BYChemRxiv

MolSanitizer: An open-source pipeline to prepare small-molecule databases for large-scale virtual screening

  • Thua-Phong Lam1,2
  • Szymon Pach1,2
  • Philip Ullmann1,2
  • Hocine El Khaoudi Enyoury3,4
  • Ruth Brenk5,6
  • Flavio Ballante7,8
  • Trent E. Balius9
  • Peter Kolb3,4
  • John Irwin10,11
  • Jens Carlsson1,2,12
  • Israel Cabeza de Vaca1,2
12 affiliations
  1. 1Department of Cell and Molecular Biology
  2. 2Uppsala University
  3. 3Institute of Pharmaceutical Chemistry
  4. 4Philipps-Universität Marburg
  5. 5Department of Biomedicine
  6. 6University of Bergen
  7. 7Department of Medical Biochemistry and Biophysics
  8. 8Karolinska Institutet
  9. 9Cancer Research Technology Program, Leidos Biomedical Research, Inc., P.O. Box B, Frederick, Maryland, 21702
  10. 10Department of Pharmaceutical Chemistry
  11. 11University of California
  12. 12Science for Life Laboratory (SciLifeLab
Open at sourcePDFDOICite

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.

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Cite

BibTeXRIS
BibTeX
@misc{lam2026molsanitizer,
  title = {{MolSanitizer: An open-source pipeline to prepare small-molecule databases for large-scale virtual screening}},
  author = {Thua-Phong Lam and Szymon Pach and Philip Ullmann and Hocine El Khaoudi Enyoury and Ruth Brenk and Flavio Ballante and Trent E. Balius and Peter Kolb and John Irwin and Jens Carlsson and Israel Cabeza de Vaca},
  howpublished = {ChemRxiv},
  year = {2026},
  month = oct,
  doi = {10.26434/chemrxiv.15010189/v1},
  url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010189/v1},
  note = {CC BY},
}
RIS
TY  - UNPB
TI  - MolSanitizer: An open-source pipeline to prepare small-molecule databases for large-scale virtual screening
AU  - Thua-Phong Lam
AU  - Szymon Pach
AU  - Philip Ullmann
AU  - Hocine El Khaoudi Enyoury
AU  - Ruth Brenk
AU  - Flavio Ballante
AU  - Trent E. Balius
AU  - Peter Kolb
AU  - John Irwin
AU  - Jens Carlsson
AU  - Israel Cabeza de Vaca
PY  - 2026
DA  - 2026/10/09
PB  - ChemRxiv
DO  - 10.26434/chemrxiv.15010189/v1
UR  - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15010189/v1
AB  - 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.
ER  -