2D

• Chem-Faiss: Chem-Faiss utilizes vector similarity search from Faiss combined with chemical fingerprinting to build a scalable similarity search architecture for compounds/molecules.
  

  

• FPSim2: FPSim2 is a RDKit-based package for fast compound similarity searches, offering high performance with high search thresholds.
  

  

• FiBeFTa: FiBeFTa is an online tool for virtual screening and fingerprint evaluation, comparing the performance of different molecular fingerprints for target-specific discernment.
  

• PyRMD: PyRMD is an AI-powered Ligand-Based Virtual Screening tool powered by machine learning, developed for fast and efficient virtual screening.
  

  

• ScreenLamp: ScreenLamp is a modular toolkit for virtual screening, offering various command-line tools for different stages of the virtual screening process.

• SmallWorld: web-based ligand similarity on a variety of commercial databases

  

• SwissSimilarity: SwissSimilarity offers an online service for small molecule similarity screening against selected compound libraries using various cheminformatics methods.

  

• WHALES: WHALES provides a virtual screening pipeline focusing on scaffold hopping and ligand-based drug discovery through a Jupyter notebook example.
  

  

• eiR: eiR is a Bioconductor package for accelerated structure similarity searching of small molecules using an embedding and indexing approach.
  

• gpusimilarity: gpusimilarity provides a GPU implementation of chemical fingerprint similarity searching for large-scale chemical libraries.
  

• pyADA: pyADA is a cheminformatics package for performing Applicability Domain Analysis of molecular fingerprints based on similarity calculation.