In the context of developing computational tools for new modalities including beyond-Ro5 molecules, in our case for peptides with variable chain topology and stereochemistry, we have adapted molecular fingerprints based on atom-pairs for large molecules such as peptides and proteins. In particular, we combined atom-pair analysis and circular substructures as encoded the Morgan fingerprint ECFP4, with the principle of data compression using MinHashing, to design MAP4, a MinHashed Atom-Pair fingerprint. MAP4 encodes all possible pairs of circular substructures up to a diameter of four bonds in a molecule. These pairs are written in the form of two canonicalized SMILES separated by the shortest topological distance, counted in bonds, between the corresponding pair of central atoms. Remarkably, MAP4 distinguishes molecular structures across different compound classes spanning from small molecules to natural products, peptides and the metabolome, for which other fingerprints such as the classical Morgan (ECFP4) and Atom Pair (AP) fingerprints fall short. In addition, MAP4 outperforms these and many other fingerprints in virtual screening benchmarks for both small molecule drugs and peptides. Similarly to commonly used molecular fingerprints however, MAP4 does not include stereochemistry (cis-trans double bonds, enantiomers and diastereomers), which is clearly an omission considering that most molecules beyond Ro5, such as diverse natural products and synthetic compounds in the public databases ChEMBL, COCONUT, and ZINC, are chiral (Figure ). To correct this omission and enable the cheminformatic analysis of compounds with multiple chiral centers such as carbohydrates and peptides, we now report MAP4C, an improved version of the MAP4 fingerprint. MAP4C includes the description of chiral centers following the Cahn-Ingold-Prelog (CIP) nomenclature in a fraction of molecular shingles (Figure ), as well as double bond stereochemistry.