A molecular fragment cheminformatics roadmap for mesoscopic simulation

• Published in: Journal of cheminformatics 2014-10, Vol.6 (1), p.45-45, Article 45
• Main Authors: Truszkowski, Andreas, Daniel, Mirco, Kuhn, Hubert, Neumann, Stefan, Steinbeck, Christoph, Zielesny, Achim, Epple, Matthias
• Format: Article
• Language: English
• Subjects: Analysis; Chemistry; Chemistry and Materials Science; Computational Biology/Bioinformatics; Computer Applications in Chemistry; Documentation and Information in Chemistry; Electrons; Methodology; Molecular dynamics; Public software; Theoretical and Computational Chemistry
• ISSN: 1758-2946; 1758-2946
• DOI: 10.1186/s13321-014-0045-3

Background Mesoscopic simulation studies the structure, dynamics and properties of large molecular ensembles with millions of atoms: Its basic interacting units (beads) are no longer the nuclei and electrons of quantum chemical ab-initio calculations or the atom types of molecular mechanics but molecular fragments, molecules or even larger molecular 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 task is a tedious, time-consuming and error-prone venture that limits its practical use and application. A consequent cheminformatics 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 Fragment Dynamics (MFD) simulation kernel to allow its efficient use and practical application. Results The molecular fragment cheminformatics roadmap consists of four consecutive building blocks: An adequate fragment structure representation (1), defined operations on these fragment structures (2), the description of compartments with defined compositions and structural alignments (3), and the graphical setup and analysis of a whole simulation box (4). The basis of the cheminformatics approach (i.e. building block 1) is a SMILES-like line notation (denoted f SMILES) with connected molecular fragments to represent a molecular structure. The f SMILES notation and the following concepts and methods for building blocks 2-4 are outlined with examples and practical usage scenarios. It is shown that the requirements of the roadmap may be partly covered by already existing open-source cheminformatics software. Conclusions Mesoscopic simulation techniques like MFD may be considerably alleviated and broadened for practical use with a consequent cheminformatics layer that successfully tackles its setup subtleties and conceptual usage hurdles. Molecular Fragment Cheminformatics may be regarded as a crucial accelerator to propagate MFD and similar mesoscopic simulation techniques in the molecular sciences. Graphical abstract A molecular fragment cheminformatics roadmap for mesoscopic simulation.