Background: Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembleswith millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemicalab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even largermolecular entities. For its simulation setup and output a mesoscopic simulation kernel software uses abstract matrix(array) representations for bead topology and connectivity. Therefore a pure kernel-based mesoscopic simulation taskis a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequentcheminformatics approach tackles these problems and provides solutions for a considerably enhanced accessibility.This study aims at outlining a complete cheminformatics roadmap that frames a mesoscopic Molecular FragmentDynamics (MFD) simulation kernel to allow its efficient use and practical application.

Results: The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: Anadequate fragment structure representation (1), defined operations on these fragment structures (2), the descriptionof compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of awhole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like linenotation (denotedfSMILES) with connected molecular fragments to represent a molecular structure. ThefSMILESnotation and the following concepts and methods for building blocks 2-4 are outlined with examples and practicalusage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existingopen-source cheminformatics software.

Conclusions: Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened forpractical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptualusage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD andsimilar mesoscopic simulation techniques in the molecular sciences.